Macromolecule Content

Total Structure Weight: 33.14 kDa
Atom Count: 2555
Modelled Residue Count: 275
Deposited Residue Count: 290
Unique protein chains: 1

3DNP

Crystal structure of Stress response protein yhaX from Bacillus subtilis

PDB DOI: 10.2210/pdb3DNP/pdb

Classification: structural genomics, unknown function
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-02 Released: 2008-07-29
Deposition Author(s): Chang, C., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Stress response protein yhaX from Bacillus subtilis

Chang, C., Tesar, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stress response protein yhaX	A	290	Bacillus subtilis	Mutation(s): 0 Gene Names: yhaX, BSU09830
UniProt
Find proteins for O07539 (Bacillus subtilis (strain 168)) Explore O07539 Go to UniProtKB: O07539
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O07539
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

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: 1.85 Å
R-Value Free: 0.207
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.939	α = 90
b = 63.939	β = 90
c = 161.485	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2008-07-02
Released Date: 2008-07-29

Deposition Author(s):

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description

RCSB PDB is 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.