2A9F | pdb_00002a9f

Crystal structure of a putative malic enzyme ((S)-malate:NAD+ oxidoreductase (decarboxylating))

• PDB DOI: https://doi.org/10.2210/pdb2A9F/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-11 Released: 2005-08-02 
• Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.304 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Crystal structure of a putative malic enzyme ((S)-malate:NAD+ oxidoreductase (decarboxylating))

Seetharaman, J., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 84.31 kDa 
• Atom Count: 5,614 
• Modeled Residue Count: 763 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative malic enzyme ((S)-malate:NAD+ oxidoreductase (decarboxylating))	A, B	398	Streptococcus pyogenes	Mutation(s): 0  EC: 1.1.1.39
UniProt
Find proteins for Q99ZS1 (Streptococcus pyogenes serotype M1) Explore Q99ZS1  Go to UniProtKB:  Q99ZS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.304 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.258	α = 90
b = 79.253	β = 90
c = 145.594	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-10-05
  Changes: Other
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references