3D5L | pdb_00003d5l

Crystal structure of regulatory protein RecX

PDB DOI: https://doi.org/10.2210/pdb3D5L/pdb

Classification: SIGNALING PROTEIN
Organism(s): Limosilactobacillus reuteri subsp. rodentium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-16 Released: 2008-06-10
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.300 (Depositor), 0.299 (DCC)
R-Value Work:
0.246 (Depositor), 0.246 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3D5L

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of DNA repair regulatory protein RecX.

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 51.29 kDa
Atom Count: 3,347
Modeled Residue Count: 402
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein RecX	A, B	221	Limosilactobacillus reuteri subsp. rodentium	Mutation(s): 0 Gene Names: Lreu23DRAFT_0930
UniProt
Find proteins for B3XNW8 (Limosilactobacillus reuteri subsp. rodentium (strain DSM 17509 / CIP 109821 / 100-23)) Explore B3XNW8 Go to UniProtKB: B3XNW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3XNW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.300 (Depositor), 0.299 (DCC)
R-Value Work: 0.246 (Depositor), 0.246 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.19	α = 90
b = 81.924	β = 90
c = 124.766	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-06-10

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-06-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-21
Changes: Data collection, Database references

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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.