2HAE | pdb_00002hae

Crystal structure of a putative malic enzyme (malate oxidoreductase)

• PDB DOI: https://doi.org/10.2210/pdb2HAE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-12 Released: 2006-07-04 
• 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: 3.13 Å
• R-Value Free: 
  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative malic enzyme (malate oxidoreductase)

Seetharaman, J., Swaminathan, S.

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: 171.28 kDa 
• Atom Count: 11,756 
• Modeled Residue Count: 1,492 
• Deposited Residue Count: 1,544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate oxidoreductase	A, B, C, D	386	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9WZ12 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ12  Go to UniProtKB:  Q9WZ12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.282 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.799	α = 90
b = 145.799	β = 90
c = 159.266	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description