1V5E | pdb_00001v5e

Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans

• PDB DOI: https://doi.org/10.2210/pdb1V5E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aerococcus viridans
• Mutation(s): No 


• Deposited: 2003-11-22 Released: 2005-06-28 
• Deposition Author(s): Hossain, M.T., Suzuki, K., Yamamoto, T., Imamura, S., Sekiguchi, T., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans

Hossain, M.T., Suzuki, K., Yamamoto, T., Imamura, S., Sekiguchi, T., Takenaka, 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 66.52 kDa 
• Atom Count: 5,390 
• Modeled Residue Count: 590 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate oxidase	A	590	Aerococcus viridans	Mutation(s): 0  EC: 1.2.3.3
UniProt
Find proteins for A9X9K8 (Aerococcus viridans) Explore A9X9K8  Go to UniProtKB:  A9X9K8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.231 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.66	α = 90
b = 106.12	β = 90
c = 155.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Hossain, M.T., Suzuki, K., Yamamoto, T., Imamura, S., Sekiguchi, T., Takenaka, A.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description