6K5X

Crystal Structure of the DNA-Binding Domain of GapR

PDB DOI: https://doi.org/10.2210/pdb6K5X/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Caulobacter vibrioides NA1000
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-31 Released: 2020-06-03
Deposition Author(s): Xia, B., Huang, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.259
R-Value Work: 0.251
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the DNA-Binding Domain of GapR

Xia, B., Huang, Q.

To be published.

Macromolecule Content

Total Structure Weight: 9.42 kDa
Atom Count: 545
Modelled Residue Count: 65
Deposited Residue Count: 80
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0335 protein CCNA_03428	A	80	Caulobacter vibrioides NA1000	Mutation(s): 0 Gene Names: CCNA_03428
UniProt
Find proteins for B8H4R9 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore B8H4R9 Go to UniProtKB: B8H4R9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8H4R9
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 B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.259
R-Value Work: 0.251
R-Value Observed: 0.251
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.422	α = 90
b = 47.422	β = 90
c = 225.502	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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 R01GM133198.