6K5X | pdb_00006k5x

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 (Depositor), 0.284 (DCC)
R-Value Work:
0.251 (Depositor), 0.264 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K5X

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
Modeled Residue Count: 65
Deposited Residue Count: 80
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.284 (DCC)
R-Value Work: 0.251 (Depositor), 0.264 (DCC)
R-Value Observed: 0.251 (Depositor)

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

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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

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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.