3BJA | pdb_00003bja

Crystal structure of putative MarR-like transcription regulator (NP_978771.1) from Bacillus cereus ATCC 10987 at 2.38 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BJA/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Bacillus cereus ATCC 10987
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-03 Released: 2007-12-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.253 (Depositor), 0.260 (DCC)
R-Value Work:
0.233 (Depositor), 0.240 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative MarR-like transcription regulator (NP_978771.1) from Bacillus cereus ATCC 10987 at 2.38 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 16.56 kDa
Atom Count: 1,136
Modeled Residue Count: 139
Deposited Residue Count: 139
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family, putative	A	139	Bacillus cereus ATCC 10987	Mutation(s): 0 Gene Names: NP_978771.1, BCE_2462
UniProt
Find proteins for Q738D3 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q738D3 Go to UniProtKB: Q738D3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q738D3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.253 (Depositor), 0.260 (DCC)
R-Value Work: 0.233 (Depositor), 0.240 (DCC)
R-Value Observed: 0.234 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BJA

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.321	α = 90
b = 71.321	β = 90
c = 65.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-11
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: 2023-01-25
Changes: Database references
Version 1.5: 2024-11-13
Changes: Data collection, Structure summary

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.