3DNP | pdb_00003dnp

Crystal structure of Stress response protein yhaX from Bacillus subtilis

• PDB DOI: https://doi.org/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of Stress response protein yhaX from Bacillus subtilis

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.14 kDa 
• Atom Count: 2,555 
• Modeled Residue Count: 275 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary