3W4Y | pdb_00003w4y

Crystal structure of yeast Erv1 core

• PDB DOI: https://doi.org/10.2210/pdb3W4Y/pdb

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


• Deposited: 2013-01-17 Released: 2013-03-20 
• Deposition Author(s): Kawano, S., Terao, K., Watanabe, N., Endo, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of yeast Erv1 core

Kawano, S., Terao, K., Watanabe, N., Endo, T.

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: 45.26 kDa 
• Atom Count: 3,338 
• Modeled Residue Count: 350 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial FAD-linked sulfhydryl oxidase ERV1	A, B, C	120	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ERV1, ERV1/YGR029W, YGR029W EC: 1.8.3.2
UniProt
Find proteins for P27882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27882  Go to UniProtKB:  P27882

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], E [auth B], F [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.531	α = 90
b = 116.222	β = 90
c = 151.119	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Kawano, S., Terao, K., Watanabe, N., Endo, T.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary