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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.141 (Depositor), 0.141 (DCC)
R-Value Work:
0.123 (Depositor), 0.124 (DCC)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6WJM

This is version 1.1 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1QJV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.141 (Depositor), 0.141 (DCC)
R-Value Work: 0.123 (Depositor), 0.124 (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

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Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.