2W2L | pdb_00002w2l

Crystal structure of the holo forms of Rhodotorula graminis D- mandelate dehydrogenase at 2.5A.

• PDB DOI: https://doi.org/10.2210/pdb2W2L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodotorula graminis
• Expression System: Escherichia coli BL21(DE3)
• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.186 (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)

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: 155.03 kDa 
• Atom Count: 11,321 
• Modeled Residue Count: 1,380 
• Deposited Residue Count: 1,392 
• Unique protein chains: 2

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.098	α = 90
b = 110.154	β = 90
c = 79.836	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	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: 2018-01-24
  Changes: Advisory, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description