[English] 日本語
- PDB-1iz8: Re-refinement of the structure of hydrolytic haloalkane dehalogen... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 1iz8
TitleRe-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution
Function / homology
Function and homology information

haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / 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
Haloalkane dehalogenase / BROMIDE ION / 1,3-PROPANDIOL / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsStreltsov, V.A.
Journal: Biochemistry / Year: 2003
Title: Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates
Authors: Streltsov, V.A. / Prokop, Z. / Damborsky, J. / Nagata, Y. / Oakley, A. / Wilce, M.C.J.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26
Authors: Marek, J. / Vevodova, J. / Smatanova, I. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J.
DepositionSep 30, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Dec 20, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Remark 0This entry 1IZ8 reflects an alternative modeling of the structural data in r1d07sf, In PDB entry ...This entry 1IZ8 reflects an alternative modeling of the structural data in r1d07sf, In PDB entry 1IZ8 information in remark 200 series is based on the experiment described in pdb entry 1D07 original data determined by author: J.MAREK,J.VEVODOVA,I.SMATANOVA,Y.NAGATA,L.A.SVENSSON,J.NEWMAN,M.TAKAGI,J.DAMBORSKY

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
hetero molecules

Theoretical massNumber of molelcules
Total (without water)33,2906

  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.227, 71.721, 73.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions











#1: Protein HALOALKANE DEHALOGENASE, LINB / / 1 / 3 / 4 / 6-tetrachloro-1 / 4-cyclohexadiene hydrolase

Mass: 33013.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Plasmid: PMYLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide

Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol

Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.2 % / Description: Author used the sf data from entry 1D07.
Crystal grow
Method: other / Details: re-refined 1D07

Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 13 Å2


RefinementResolution: 2→17.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1958543.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1210 8.3 %RANDOM
Rwork0.166 ---
obs-14610 79 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 122.835 Å2 / ksol: 0.441396 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---3.36 Å20 Å2
3---3.94 Å2
Refine analyze
Luzzati coordinate error0.28 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→17.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 9 310 2641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2→2.2 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.303 264 7.9 %
Rwork0.199 3070 -
obs--73.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

About Yorodumi


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


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