2W2K | pdb_00002w2k

Crystal structure of the apo forms of Rhodotorula graminis D- mandelate dehydrogenase at 1.8A.

• PDB DOI: https://doi.org/10.2210/pdb2W2K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodotorula graminis
• Mutation(s): No 


• Deposited: 2008-11-02 Released: 2009-11-17 
• Deposition Author(s): Vachieri, S.G., Cole, A.R., Bagneris, C., Baker, D.P., Fewson, C.A., Basak, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Apo and Holo Forms of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase

Vachieri, S.G., Cole, A.R., Bagneris, C., Baker, D.P., Fewson, C.A., Basak, A.K.

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: 75.98 kDa 
• Atom Count: 6,062 
• Modeled Residue Count: 689 
• Deposited Residue Count: 696 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-MANDELATE DEHYDROGENASE	A	348	Rhodotorula graminis	Mutation(s): 0
UniProt
Find proteins for Q7LLW9 (Rhodotorula graminis) Explore Q7LLW9  Go to UniProtKB:  Q7LLW9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-MANDELATE DEHYDROGENASE	B	348	Rhodotorula graminis	Mutation(s): 0
UniProt
Find proteins for Q7LLW9 (Rhodotorula graminis) Explore Q7LLW9  Go to UniProtKB:  Q7LLW9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.03	α = 90
b = 81.071	β = 96.27
c = 93.955	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Vachieri, S.G., Cole, A.R., Bagneris, C., Baker, D.P., Fewson, C.A., Basak, A.K.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description