[English] 日本語
Yorodumi
- PDB-3hwc: Crystal Structure of Chlorophenol 4-Monooxygenase (TftD) of Burkh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hwc
TitleCrystal Structure of Chlorophenol 4-Monooxygenase (TftD) of Burkholderia cepacia AC1100
ComponentsChlorophenol-4-monooxygenase component 2
KeywordsOXIDOREDUCTASE / beta barrel / helix bundle / Monooxygenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / : / oxidoreductase activity, acting on the CH-CH group of donors / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / : / protein homotetramerization
Similarity search - Function
4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 ...4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FADH(2)-dependent monooxygenase TftD
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBallinger, J.W. / Kang, C.H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100.
Authors: Webb, B.N. / Ballinger, J.W. / Kim, E. / Belchik, S.M. / Lam, K.S. / Youn, B. / Nissen, M.S. / Xun, L. / Kang, C.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chlorophenol-4-monooxygenase component 2
B: Chlorophenol-4-monooxygenase component 2
C: Chlorophenol-4-monooxygenase component 2
D: Chlorophenol-4-monooxygenase component 2


Theoretical massNumber of molelcules
Total (without water)230,0864
Polymers230,0864
Non-polymers00
Water21,2581180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23620 Å2
ΔGint-186 kcal/mol
Surface area62810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.198, 149.867, 212.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Chlorophenol-4-monooxygenase component 2


Mass: 57521.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: AC1100 / Gene: tftD / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O87009
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1180 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20% (w/v) PEG 4000, 0.2M lithium nitrate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97956, 0.91840, 0.97934
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.91841
30.979341
ReflectionResolution: 2→47.34 Å / Observed criterion σ(F): 0.01 / Observed criterion σ(I): 3
Reflection shellResolution: 2→2.05 Å / % possible all: 20

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CrystalCleardata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.942 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.5 / σ(F): 0.01 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1015 1.27 %
Rwork0.1676 --
obs0.1684 79750 97.99 %
all-80765 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.619 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 33.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.067 Å2-0 Å2-0 Å2
2---8.137 Å2-0 Å2
3----5.259 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15336 0 0 1180 16516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415720
X-RAY DIFFRACTIONf_angle_d0.75721340
X-RAY DIFFRACTIONf_dihedral_angle_d16.6715684
X-RAY DIFFRACTIONf_chiral_restr0.0562288
X-RAY DIFFRACTIONf_plane_restr0.0032820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63150.24861430.175311006X-RAY DIFFRACTION97
2.6315-2.7960.22771410.175911001X-RAY DIFFRACTION97
2.796-3.01120.23981460.175911134X-RAY DIFFRACTION98
3.0112-3.3130.27041450.178911180X-RAY DIFFRACTION98
3.313-3.78950.23591470.169111337X-RAY DIFFRACTION99
3.7895-4.76360.1871420.147111398X-RAY DIFFRACTION99
4.7636-19.94270.20171510.163311679X-RAY DIFFRACTION99

+
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://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