3RJU | pdb_00003rju

Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate

• PDB DOI: https://doi.org/10.2210/pdb3RJU/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2011-04-27 
• Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate

Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 39.12 kDa 
• Atom Count: 3,356 
• Modeled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase/D-alanine Carboxypeptidase	A	351	Yersinia pestis CO92	Mutation(s): 0  Gene Names: ampH, y2964, YPO1224, YP_0915
UniProt
Find proteins for Q0WHI2 (Yersinia pestis) Explore Q0WHI2  Go to UniProtKB:  Q0WHI2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rju

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.161	α = 90
b = 75.477	β = 103.93
c = 59.068	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Kim, Y., Zhou, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary