[English] 日本語
Yorodumi
- PDB-6esd: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6esd
TitleCrystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum
ComponentsFlavin-dependent L-tryptophan oxidase VioA
KeywordsBIOSYNTHETIC PROTEIN / Violacein biosynthesis / L-tryptophan oxidase
Function / homology7-chloro-L-tryptophan oxidase / Amine oxidase / Flavin containing amine oxidoreductase / antibiotic biosynthetic process / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent L-tryptophan oxidase VioA
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLai, H.E. / Morgan, M. / Moore, S. / Freemont, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
CitationJournal: Biorxiv / Year: 2017
Title: A semi-synthetic strategy for derivatization of the violacein natural product scaffold
Authors: Lai, H.E. / Chee, S.M. / Morgan, M. / Moore, S. / Polizzi, K. / Freemont, P.
History
DepositionOct 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Flavin-dependent L-tryptophan oxidase VioA
A: Flavin-dependent L-tryptophan oxidase VioA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8626
Polymers93,2202
Non-polymers1,6424
Water88349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SEC-MALS experiment reveals a dimeric assembly of VioA in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-46 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.610, 172.600, 94.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Flavin-dependent L-tryptophan oxidase VioA


Mass: 46609.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: vioA, CV_3274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 9% PEG 8000 and 9% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.6→63.78 Å / Num. obs: 38134 / % possible obs: 99 % / Redundancy: 4.55 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04776 / Rrim(I) all: 0.05391 / Net I/σ(I): 24.35
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 4.02 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.34 / Num. unique obs: 3731 / CC1/2: 0.907 / Rrim(I) all: 0.3465 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0V

3x0v


Resolution: 2.6→63.778 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.2588 1958 5.14 %
Rwork0.2088 --
obs0.2113 38070 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→63.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 108 49 6333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096457
X-RAY DIFFRACTIONf_angle_d1.1358783
X-RAY DIFFRACTIONf_dihedral_angle_d13.2723703
X-RAY DIFFRACTIONf_chiral_restr0.055933
X-RAY DIFFRACTIONf_plane_restr0.0061123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66520.39811370.31292542X-RAY DIFFRACTION98
2.6652-2.73720.37141340.29382532X-RAY DIFFRACTION99
2.7372-2.81780.35321320.28572568X-RAY DIFFRACTION99
2.8178-2.90870.36191550.26472533X-RAY DIFFRACTION99
2.9087-3.01270.30511430.26092550X-RAY DIFFRACTION99
3.0127-3.13330.331390.25082507X-RAY DIFFRACTION97
3.1333-3.27590.30681350.23832577X-RAY DIFFRACTION99
3.2759-3.44860.24991300.22552594X-RAY DIFFRACTION99
3.4486-3.66460.28571430.22222586X-RAY DIFFRACTION99
3.6646-3.94760.23221540.19792573X-RAY DIFFRACTION99
3.9476-4.34470.25651430.1682575X-RAY DIFFRACTION98
4.3447-4.97320.1981460.1662622X-RAY DIFFRACTION100
4.9732-6.26490.22561340.19032606X-RAY DIFFRACTION98
6.2649-63.79670.2011330.18422747X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more