3TL2 | pdb_00003tl2

Crystal structure of Bacillus anthracis str. Ames malate dehydrogenase in closed conformation.

• PDB DOI: https://doi.org/10.2210/pdb3TL2/pdb

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


• Deposited: 2011-08-29 Released: 2011-09-21 
• Deposition Author(s): Blus, B.J., Chruszcz, M., Tkaczuk, K.L., Osinski, T., Cymborowski, M., Kudritska, M., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus anthracis str. Ames malate dehydrogenase in closed conformation.

Blus, B.J., Chruszcz, M., Tkaczuk, K.L., Osinski, T., Cymborowski, M., Kudritska, M., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W.

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: 34.05 kDa 
• Atom Count: 2,808 
• Modeled Residue Count: 312 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A	315	Bacillus anthracis	Mutation(s): 0  Gene Names: BAS4486, BA_4837, GBAA_4837, mdh EC: 1.1.1.37
UniProt
Find proteins for Q6HSF4 (Bacillus anthracis) Explore Q6HSF4  Go to UniProtKB:  Q6HSF4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	C [auth A], E [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TL2

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.181	α = 90
b = 68.377	β = 90
c = 142.919	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Blus, B.J., Chruszcz, M., Tkaczuk, K.L., Osinski, T., Cymborowski, M., Kudritska, M., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Refinement description