1Z2I | pdb_00001z2i

CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

• PDB DOI: https://doi.org/10.2210/pdb1Z2I/pdb

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


• Deposited: 2005-03-08 Released: 2005-03-15 
• Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal Structure of Agrobacterium Tumefaciens Malate Dehydrogenase

Patskovsky, Y., Almo, S.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.85 kDa 
• Atom Count: 11,399 
• Modeled Residue Count: 1,400 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
malate dehydrogenase	A, B, C, D	358	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: AGR_L_3209
UniProt
Find proteins for Q7CRW4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CRW4  Go to UniProtKB:  Q7CRW4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 98.22	β = 90
c = 146.47	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-03-15
  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: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references