6WJM | pdb_00006wjm

The crystal structure beta-lactamase from Desulfarculus baarsii DSM 2075

• PDB DOI: https://doi.org/10.2210/pdb6WJM/pdb

• Classification: HYDROLASE
• Organism(s): Desulfarculus baarsii DSM 2075
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-14 Released: 2020-04-22 
• Deposition Author(s): Chang, C., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

The crystal structure beta-lactamase from Desulfarculus baarsii DSM 2075

Chang, C., Welk, L., Endres, M., 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: 31.29 kDa 
• Atom Count: 2,538 
• Modeled Residue Count: 269 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	298	Desulfarculus baarsii DSM 2075	Mutation(s): 0  Gene Names: Deba_2488 EC: 3.5.2.6
UniProt
Find proteins for E1QJV5 (Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14)) Explore E1QJV5  Go to UniProtKB:  E1QJV5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ALA	B [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.722	α = 90
b = 73.46	β = 110.3
c = 42.923	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Chang, C., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description