3D19

Crystal structure of a conserved metalloprotein from Bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb3D19/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus cereus G9241
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-05 Released: 2008-07-08 
• Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

Literature

Crystal structure of a conserved metalloprotein from Bacillus cereus.

Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 200.51 kDa 
• Atom Count: 13,109 
• Modelled Residue Count: 1,558 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved metalloprotein	A, B, C, D, E, F	283	Bacillus cereus G9241	Mutation(s): 5  Gene Names: BCE_G9241_1042

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.825	α = 90
b = 136.378	β = 102.84
c = 87.06	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Freeman, J., Bain, K.T., Chang, S., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references