4DF9 | pdb_00004df9

Crystal structure of a putative peptidase (BF3526) from Bacteroides fragilis NCTC 9343 at 2.17 A resolution

PDB DOI: https://doi.org/10.2210/pdb4DF9/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-23 Released: 2012-02-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative peptidase (BF3526) from Bacteroides fragilis NCTC 9343 at 2.17 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 285.85 kDa
Atom Count: 21,813
Modeled Residue Count: 2,421
Deposited Residue Count: 2,454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative peptidase	A, B, C, D, E A, B, C, D, E, F	409	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF3526, BF9343_3433
UniProt
Find proteins for Q5L9L3 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5L9L3 Go to UniProtKB: Q5L9L3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5L9L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain MB [auth E] SDF format, chain R [auth B] SDF format, chain SA [auth D] SDF format, chain XB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MB [auth E] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain XB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MB [auth E] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain XB [auth F]	FA [auth C] J [auth A] MB [auth E] R [auth B] SA [auth D] FA [auth C], J [auth A], MB [auth E], R [auth B], SA [auth D], XB [auth F]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain J [auth A] Focus chain MB [auth E] Focus chain R [auth B] Focus chain SA [auth D] Focus chain XB [auth F] Interactions & Density Focus chain FA [auth C] Focus chain J [auth A] Focus chain MB [auth E] Focus chain R [auth B] Focus chain SA [auth D] Focus chain XB [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NB [auth E] SDF format, chain TA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain TA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain TA [auth D]	GA [auth C], K [auth A], L [auth A], NB [auth E], TA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain NB [auth E] Focus chain TA [auth D] Interactions & Density Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain NB [auth E] Focus chain TA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain AC [auth F] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OB [auth E] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain RB [auth E] SDF format, chain S [auth B] SDF format, chain SB [auth E] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain YB [auth F] SDF format, chain ZA [auth D] SDF format, chain ZB [auth F] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OB [auth E] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain RB [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth E] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth F] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth F] mmCIF format, chain AB [auth D] mmCIF format, chain AC [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OB [auth E] mmCIF format, chain PB [auth E] mmCIF format, chain QB [auth E] mmCIF format, chain RB [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SB [auth E] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain YB [auth F] mmCIF format, chain ZA [auth D] mmCIF format, chain ZB [auth F]	AB [auth D] AC [auth F] BB [auth D] CB [auth D] DB [auth D] AB [auth D], AC [auth F], BB [auth D], CB [auth D], DB [auth D], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], M [auth A], MA [auth C], NA [auth C], OB [auth E], PB [auth E], QB [auth E], RB [auth E], S [auth B], SB [auth E], T [auth B], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], XA [auth D], YA [auth D], YB [auth F], ZA [auth D], ZB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth E] Focus chain S [auth B] Focus chain SB [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth E] Focus chain S [auth B] Focus chain SB [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain VB [auth F] SDF format, chain WB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain VB [auth F] MOL2 format, chain WB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain LB [auth E] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain VB [auth F] mmCIF format, chain WB [auth F]	DA [auth C] EA [auth C] H [auth A] I [auth A] KB [auth E] DA [auth C], EA [auth C], H [auth A], I [auth A], KB [auth E], LB [auth E], P [auth B], Q [auth B], QA [auth D], RA [auth D], VB [auth F], WB [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain VB [auth F] Focus chain WB [auth F] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain VB [auth F] Focus chain WB [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain BC [auth F] SDF format, chain CC [auth F] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain N [auth A] SDF format, chain OA [auth C] SDF format, chain TB [auth E] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth F] MOL2 format, chain CC [auth F] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain TB [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain BC [auth F] mmCIF format, chain CC [auth F] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain TB [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] BC [auth F] CC [auth F] EB [auth D] AA [auth B], BA [auth B], BC [auth F], CC [auth F], EB [auth D], FB [auth D], GB [auth D], HB [auth D], IB [auth D], N [auth A], OA [auth C], TB [auth E], X [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain CC [auth F] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain N [auth A] Focus chain OA [auth C] Focus chain TB [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain CC [auth F] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain N [auth A] Focus chain OA [auth C] Focus chain TB [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain JB [auth E] SDF format, chain O [auth B] SDF format, chain PA [auth D] SDF format, chain UB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain UB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain UB [auth F]	CA [auth C] G [auth A] JB [auth E] O [auth B] PA [auth D] CA [auth C], G [auth A], JB [auth E], O [auth B], PA [auth D], UB [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain G [auth A] Focus chain JB [auth E] Focus chain O [auth B] Focus chain PA [auth D] Focus chain UB [auth F] Interactions & Density Focus chain CA [auth C] Focus chain G [auth A] Focus chain JB [auth E] Focus chain O [auth B] Focus chain PA [auth D] Focus chain UB [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34DF9

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.73	α = 90
b = 92.82	β = 125.26
c = 173.89	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Data collection, Structure summary