3KZV | pdb_00003kzv

The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3KZV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-08 Released: 2010-03-02 
• Deposition Author(s): Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae

Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

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: 27.78 kDa 
• Atom Count: 2,033 
• Modeled Residue Count: 249 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YIR035C	A	254	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: GI:6322226, YIR035C EC: 1 (PDB Primary Data), 1.1.1.320 (UniProt)
UniProt
Find proteins for P40579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40579  Go to UniProtKB:  P40579

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.413	α = 90
b = 117.413	β = 90
c = 89.488	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Zhang, R., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations