4FUU | pdb_00004fuu

Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4FUU/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-28 Released: 2012-10-31 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Literature

Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.94 kDa 
• Atom Count: 2,703 
• Modeled Residue Count: 290 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine aminopeptidase	A	309	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_2548
UniProt
Find proteins for Q8A4P9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A4P9  Go to UniProtKB:  Q8A4P9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34FUU

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.236	α = 65.47
b = 41.582	β = 80.43
c = 48.528	γ = 78.68

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary