3IMF | pdb_00003imf

1.99 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor'

• PDB DOI: https://doi.org/10.2210/pdb3IMF/pdb

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


• Deposited: 2009-08-10 Released: 2009-08-18 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Gordon, E., Peterson, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.206 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

1.99 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor'

Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Gordon, E., Peterson, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

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: 113.79 kDa 
• Atom Count: 8,338 
• Modeled Residue Count: 986 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D	257	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0  Gene Names: BAS3900, BA_4204, GBAA4204, GBAA_4204, YP_020848
UniProt
Find proteins for A0A6L8NTZ6 (Bacillus anthracis) Explore A0A6L8NTZ6  Go to UniProtKB:  A0A6L8NTZ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth B], F [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.206 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33imf

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.237	α = 90
b = 89.56	β = 111.6
c = 71.785	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Halavaty, A.S., Minasov, G., Skarina, T., Onopriyenko, O., Gordon, E., Peterson, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary