3ICC

Crystal structure of a putative 3-oxoacyl-(acyl carrier protein) reductase from Bacillus anthracis at 1.87 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ICC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus anthracis str. 'Ames Ancestor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-17 Released: 2009-07-28 
• Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Cymborowski, M., Luo, H.-B., Skarina, T., Gordon, S., Savchenko, A., Edwards, A.M., Anderson, W., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis.

Hou, J., Wojciechowska, K., Zheng, H., Chruszcz, M., Cooper, D.R., Cymborowski, M., Skarina, T., Gordon, E., Luo, H., Savchenko, A., Minor, W.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 632-637

• PubMed: 22684058 
• DOI: https://doi.org/10.1107/S1744309112017939
• Primary Citation of Related Structures:  
  3ICC


• PubMed Abstract: 
  

  The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain `Ames Ancestor' complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn.

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Organizational Affiliation: 

Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 57.37 kDa 
• Atom Count: 4,279 
• Modelled Residue Count: 510 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 3-oxoacyl-(acyl carrier protein) reductase	A, B	255	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0  Gene Names: BAS1712, BA_1847, GBAA1847, GBAA_1847
UniProt
Find proteins for A0A6L7HAY4 (Bacillus anthracis) Explore A0A6L7HAY4  Go to UniProtKB:  A0A6L7HAY4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], J [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MES	K [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A], H [auth B], I [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: 1.87 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33ICC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.734	α = 90
b = 104.835	β = 90
c = 103.684	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
CCP4	model building
SOLVE	phasing
RESOLVE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
CCP4	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Cymborowski, M., Luo, H.-B., Skarina, T., Gordon, S., Savchenko, A., Edwards, A.M., Anderson, W., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-06-06
  Changes: Database references
• Version 1.3: 2012-12-26
  Changes: Database references
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary