2ZF4 | pdb_00002zf4

Crystal Structure of VioE complexed with phenylpyruvic acid

• PDB DOI: https://doi.org/10.2210/pdb2ZF4/pdb

• Classification: ANTIBIOTIC
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-20 Released: 2008-01-01 
• Deposition Author(s): Hirano, S., Shiro, Y., Nagano, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of VioE, a key player in the construction of the molecular skeleton of violacein

Hirano, S., Asamizu, S., Onaka, H., Shiro, Y., Nagano, S.

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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 134.5 kDa 
• Atom Count: 9,238 
• Modeled Residue Count: 1,087 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein VioE	A, B, C, D, E, F	194	Chromobacterium violaceum	Mutation(s): 0
UniProt
Find proteins for Q7NSZ5 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NSZ5  Go to UniProtKB:  Q7NSZ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPY	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	3-PHENYLPYRUVIC ACID C9 H8 O3 BTNMPGBKDVTSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.415	α = 90
b = 91.03	β = 90
c = 158.999	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Hirano, S., Shiro, Y., Nagano, S.

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description