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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.254 (Depositor), 0.260 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein VioE	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NSZ5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPY Query on PPY Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.254 (Depositor), 0.260 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-01

Deposition Author(s):

Hirano, S.

Shiro, Y.

Nagano, S.

Revision History (Full details and data files)

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

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Help and Resources

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Crystal Structure of VioE complexed with phenylpyruvic acid

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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