3HWU | pdb_00003hwu

Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HWU/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-18 Released: 2009-06-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.140 (Depositor), 0.140 (DCC)
R-Value Work:
0.119 (Depositor), 0.120 (DCC)
R-Value Observed:
0.121 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutropha JMP134 at 1.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 16.39 kDa
Atom Count: 1,397
Modeled Residue Count: 144
Deposited Residue Count: 147
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA-binding protein	A	147	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: Reut_B5223, YP_299413.1
UniProt
Find proteins for Q46QL5 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46QL5 Go to UniProtKB: Q46QL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46QL5
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: 1.30 Å
R-Value Free: 0.140 (Depositor), 0.140 (DCC)
R-Value Work: 0.119 (Depositor), 0.120 (DCC)
R-Value Observed: 0.121 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33HWU

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.897	α = 90
b = 53.897	β = 90
c = 111.1	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-11-06
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.