3BPK | pdb_00003bpk

Crystal structure of nitrilotriacetate monooxygenase component B from Bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb3BPK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-18 Released: 2008-01-01 
• Deposition Author(s): Osipiuk, J., Quartey, P., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.187 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

X-ray crystal structure of nitrilotriacetate monooxygenase component B from Bacillus cereus.

Osipiuk, J., Quartey, P., Abdullah, J., 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: 45.47 kDa 
• Atom Count: 4,003 
• Modeled Residue Count: 398 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrilotriacetate monooxygenase component B	A, B	206	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_5322 EC: 1.14.13
UniProt
Find proteins for Q814U7 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q814U7  Go to UniProtKB:  Q814U7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.187 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.807	α = 90
b = 76.807	β = 90
c = 295.788	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Osipiuk, J., Quartey, P., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary