3N73

Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus

• PDB DOI: https://doi.org/10.2210/pdb3N73/pdb

• Classification: LYASE
• Organism(s): Bacillus cereus ATCC 10987
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-26 Released: 2010-06-09 
• Deposition Author(s): Cabello, R., Chruszcz, M., Xu, X., Zimmerman, M.D., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.221 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus

Cabello, R., Chruszcz, M., Xu, X., Zimmerman, M.D., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.48 kDa 
• Atom Count: 4,105 
• Modelled Residue Count: 499 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 4-hydroxy-2-oxoglutarate aldolase	A, B	251	Bacillus cereus ATCC 10987	Mutation(s): 0  Gene Names: BCE_5001
UniProt
Find proteins for Q72YM0 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q72YM0  Go to UniProtKB:  Q72YM0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [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: 2.07 Å
• R-Value Free:  0.221 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.066	α = 90
b = 166.644	β = 90
c = 37.279	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Cabello, R., Chruszcz, M., Xu, X., Zimmerman, M.D., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Structure summary