3OAJ | pdb_00003oaj

CRYSTAL STRUCTURE OF putative dioxygenase from Bacillus subtilis subsp. subtilis str. 168

• PDB DOI: https://doi.org/10.2210/pdb3OAJ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-05 Released: 2010-08-18 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.225 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF putative dioxygenase from Bacillus subtilis subsp. subtilis str. 168

Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 76.36 kDa 
• Atom Count: 5,692 
• Modeled Residue Count: 620 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ring-cleaving dioxygenase mhqO	A, B	335	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU05490, CAB12356.1, mhqO, ydfO EC: 1.13.11
UniProt
Find proteins for P96693 (Bacillus subtilis (strain 168)) Explore P96693  Go to UniProtKB:  P96693

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.215	α = 90
b = 86.181	β = 91.65
c = 72.968	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description