2W2L

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), 0.260 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 155.03 kDa
Atom Count: 11,321
Modelled Residue Count: 1,380
Deposited Residue Count: 1,392
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7LLW9
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7LLW9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.265 (Depositor), 0.260 (DCC)
R-Value Work: 0.182 (Depositor), 0.180 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Revision History (Full details and data files)

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