3CJM | pdb_00003cjm

Crystal structure of putative beta-lactamase (NP_815223.1) from Enterococcus faecalis V583 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CJM/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-13 Released: 2008-03-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of putative beta-lactamase (NP_815223.1) from Enterococcus faecalis V583 at 1.50 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.67 kDa 
• Atom Count: 2,510 
• Modeled Residue Count: 255 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative beta-lactamase	A	282	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: NP_815223.1, EF_1502
UniProt
Find proteins for Q834X5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834X5  Go to UniProtKB:  Q834X5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth A], C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-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:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CJM

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.975	α = 90
b = 64.975	β = 90
c = 140.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  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, Structure summary