3C4A | pdb_00003c4a

Crystal structure of vioD hydroxylase in complex with FAD from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR158

PDB DOI: https://doi.org/10.2210/pdb3C4A/pdb

Classification: OXIDOREDUCTASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-29 Released: 2008-02-05
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Janjua, H., Xiao, R., Maglaqui, M., Wang, H., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.262 (Depositor), 0.276 (DCC)
R-Value Work:
0.202 (Depositor), 0.215 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of vioD hydroxylase in complex with FAD from Chromobacterium violaceum.

Forouhar, F., Neely, H., Seetharaman, J., Janjua, H., Xiao, R., Maglaqui, M., Wang, H., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 43.95 kDa
Atom Count: 3,009
Modeled Residue Count: 365
Deposited Residue Count: 381
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable tryptophan hydroxylase vioD	A	381	Chromobacterium violaceum ATCC 12472	Mutation(s): 0 Gene Names: vioD, CV_3271 EC: 1 (PDB Primary Data), 1.14.13.217 (UniProt)
UniProt
Find proteins for Q9S3U8 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q9S3U8 Go to UniProtKB: Q9S3U8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S3U8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262 (Depositor), 0.276 (DCC)
R-Value Work: 0.202 (Depositor), 0.215 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.179	α = 90
b = 97.725	β = 90
c = 40.605	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary