3MDO | pdb_00003mdo

Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from Parabacteroides distasonis ATCC 8503 at 1.91 A resolution

PDB DOI: https://doi.org/10.2210/pdb3MDO/pdb

Classification: LIGASE
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-30 Released: 2010-06-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.190 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.170 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from Parabacteroides distasonis ATCC 8503 at 1.91 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 89.68 kDa
Atom Count: 6,351
Modeled Residue Count: 728
Deposited Residue Count: 778
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 phosphoribosylformylglycinamidine cyclo-ligase	A, B	389	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_2101 EC: 6.3.3.1
UniProt
Find proteins for A6LDR8 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LDR8 Go to UniProtKB: A6LDR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LDR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B]	HA [auth B], IA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	EA [auth B], FA [auth B], GA [auth B], P [auth A], Q [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain P [auth A] Focus chain Q [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] J [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Y [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Y [auth B]	I [auth A], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain Y [auth B] Interactions & Density Focus chain I [auth A] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] S [auth B] C [auth A], D [auth A], E [auth A], F [auth A], S [auth B], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain V [auth B] Focus chain W [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.190 (Depositor), 0.200 (DCC)
R-Value Work: 0.154 (Depositor), 0.170 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33MDO

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.945	α = 90
b = 99.945	β = 90
c = 163.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary