8JRC

Crystal structure of the GAF domain of the transcriptional activator NifA

PDB DOI: https://doi.org/10.2210/pdb8JRC/pdb

Classification: TRANSCRIPTION
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-16 Released: 2024-06-19
Deposition Author(s): Zeng, Y., Guo, L., Li, D.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.259
R-Value Work: 0.206
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the GAF domain of the transcriptional activator NifA

Zeng, Y., Guo, L., Li, D.F.

To be published.

Macromolecule Content

Total Structure Weight: 46.03 kDa
Atom Count: 2,687
Modelled Residue Count: 344
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nif-specific regulatory protein	A, B	209	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: nifA
UniProt
Find proteins for A0A2P0ZWG8 (Rhodopseudomonas palustris) Explore A0A2P0ZWG8 Go to UniProtKB: A0A2P0ZWG8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2P0ZWG8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.259
R-Value Work: 0.206
R-Value Observed: 0.209
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.631	α = 90
b = 70.093	β = 113.06
c = 55.039	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91851102

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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.