[English] 日本語
Yorodumi
- PDB-1cij: HALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cij
TitleHALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE
ComponentsPROTEIN (HALOALKANE DEHALOGENASE)
KeywordsHYDROLASE / DEHALOGENASE / COLLISION COMPLEX / ALPHA/BETA-HYDROLASE
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsRidder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase.
Authors: Pikkemaat, M.G. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B.
#1: Journal: Nature / Year: 1993
Title: Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.
Authors: Verschueren, K.H. / Seljee, F. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism.
Authors: Verschueren, K.H. / Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#3: Journal: Embo J. / Year: 1991
Title: Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes.
Authors: Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
Authors: Rozeboom, H.J. / Kingma, J. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMar 31, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (HALOALKANE DEHALOGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4014
Polymers35,1621
Non-polymers2403
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.407, 71.964, 40.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PROTEIN (HALOALKANE DEHALOGENASE) / DHLA


Mass: 35161.770 Da / Num. of mol.: 1 / Mutation: I2V
Source method: isolated from a genetically manipulated source
Details: BROMIDE ION / Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Production host: Escherichia coli (E. coli) / References: UniProt: P22643, haloalkane dehalogenase
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCY AT 2 IS DUE TO EXPRESSION SYSTEM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34 %
Crystal growpH: 5.8
Details: 50 % AMMONIUM SULFATE 100 MM MES BUFFER, PH 5.9 , pH 5.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.9 / PH range high: 5.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
2100 mMMES1drop
347-53 %ammonium sulfate1reservoir
4100 mMMES1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 24, 1997 / Details: DOUBLE MIRRORS (MAC-XOS)
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12688 / % possible obs: 97.6 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.108 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.363 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 34688 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.363

-
Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BE0
Resolution: 2.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED
Cross valid method: THROUGHOUT, EXCEPT LAST STEP IN WHICH ALL DATA (WORK+TEST SET) WERE USED
σ(F): 0
Details: THE VALUES LISTED AS WORKING IN REMARK 3 APPLY TO THE LAST CYCLE OF THE REFINEMENT IN WHICH ALL DATA (WORK + FREE) WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1000 7.8 %RANDOM EXTENSION OF SET USED FOR 1BE0 MODEL
Rwork0.226 ---
obs-11923 93.1 %-
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 3 160 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.831.5
X-RAY DIFFRACTIONx_mcangle_it4.182
X-RAY DIFFRACTIONx_scbond_it4.12
X-RAY DIFFRACTIONx_scangle_it5.552.5
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 125 8.8 %
Rwork0.305 1299 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 8.8 % / Rfactor Rwork: 0.305

+
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