3K9I

Crystal structure of Putative protein binding protein (NP_241345.1) from Bacillus halodurans at 2.71 A resolution

PDB DOI: https://doi.org/10.2210/pdb3K9I/pdb

Classification: PROTEIN BINDING
Organism(s): Halalkalibacterium halodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-15 Released: 2009-11-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.233
R-Value Work: 0.221
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative protein binding protein (NP_241345.1) from Bacillus halodurans at 2.71 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 13.13 kDa
Atom Count: 874
Modelled Residue Count: 110
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0479 protein	A	117	Halalkalibacterium halodurans	Mutation(s): 0 Gene Names: BH0479
UniProt
Find proteins for Q9KFK0 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFK0 Go to UniProtKB: Q9KFK0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KFK0
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: 2.71 Å
R-Value Free: 0.233
R-Value Work: 0.221
R-Value Observed: 0.221
Space Group: P 6₁ 2 2
Diffraction Data: https://doi.org/10.18430/M33K9I

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.656	α = 90
b = 73.656	β = 90
c = 115.838	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: 2009-11-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.