[English] 日本語
Yorodumi
- PDB-4lbp: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burk... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lbp
Title5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Complex with 2,5-dihydroxybenzoquinone
Components5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
KeywordsLYASE
Function / homologyYCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 2,5-dihydroxycyclohexa-2,5-diene-1,4-dione / YCII-related domain-containing protein
Function and homology information
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Catalytic Mechanism of 5-Chlorohydroxyhydroquinone Dehydrochlorinase from the YCII Superfamily of Largely Unknown Function.
Authors: Hayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4622
Polymers11,3221
Non-polymers1401
Water1,40578
1
A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules

A: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8508
Polymers45,2894
Non-polymers5604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation12_565x,x-y+1,-z1
Buried area8440 Å2
ΔGint-35 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.191, 90.191, 50.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-347-

HOH

31A-364-

HOH

-
Components

#1: Protein 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)


Mass: 11322.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45075
#2: Chemical ChemComp-1WG / 2,5-dihydroxycyclohexa-2,5-diene-1,4-dione / 2,5-dihydroxybenzoquinone


Mass: 140.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (w/v) polyethylene glycol 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 10578 / Num. obs: 10578 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.87-1.91100
1.9-1.941100
1.94-1.971100
1.97-2.011100
2.01-2.061100
2.06-2.111100

-
Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→45.096 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 1058 10.01 %
Rwork0.1887 --
obs0.1917 10571 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→45.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 10 78 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007813
X-RAY DIFFRACTIONf_angle_d1.0561100
X-RAY DIFFRACTIONf_dihedral_angle_d12.036293
X-RAY DIFFRACTIONf_chiral_restr0.079115
X-RAY DIFFRACTIONf_plane_restr0.004142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9540.24561300.1891167X-RAY DIFFRACTION100
1.954-2.0570.2331280.17661147X-RAY DIFFRACTION100
2.057-2.18590.24681270.19081154X-RAY DIFFRACTION100
2.1859-2.35470.1881320.19781175X-RAY DIFFRACTION100
2.3547-2.59160.23691300.19821177X-RAY DIFFRACTION100
2.5916-2.96660.22851320.19671186X-RAY DIFFRACTION100
2.9666-3.73730.22261340.19341203X-RAY DIFFRACTION100
3.7373-45.0960.2061450.1791304X-RAY DIFFRACTION100

+
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