[English] 日本語
Yorodumi
- PDB-1bn6: HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bn6
TitleHALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / DEHALOGENASE / ALPHA/BETA-HYDROLASE / DHLA
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
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
Similarity search - Component
Biological speciesRhodococcus sp. (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNewman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
CitationJournal: Biochemistry / Year: 1999
Title: Haloalkane dehalogenases: structure of a Rhodococcus enzyme.
Authors: Newman, J. / Peat, T.S. / Richard, R. / Kan, L. / Swanson, P.E. / Affholter, J.A. / Holmes, I.H. / Schindler, J.F. / Unkefer, C.J. / Terwilliger, T.C.
History
DepositionJul 31, 1998Processing site: BNL
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)33,3671
Polymers33,3671
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.520, 79.970, 43.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein HALOALKANE DEHALOGENASE /


Mass: 33367.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (unknown) / Production host: Escherichia coli (E. coli) / References: UniProt: P59336, haloalkane dehalogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.43 Å3/Da / Density % sol: 38.8 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMTris-SO41drop
325 %PEG15001reservoir
40.1 MMES1reservoir
50.3 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8157
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 53599 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 9
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.264 / % possible all: 83.6
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 83.6 % / Rmerge(I) obs: 0.264

-
Processing

Software
NameVersionClassification
CNS0.3refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL AT PH 5.5

Resolution: 1.5→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2577 5 %RANDOM
Rwork0.167 ---
obs0.167 51084 96.8 %-
Solvent computationBsol: 28.53 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.413 Å20 Å20 Å2
2---0.224 Å20 Å2
3----0.189 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 4 329 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.033
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.411.5
X-RAY DIFFRACTIONc_mcangle_it0.692
X-RAY DIFFRACTIONc_scbond_it0.52
X-RAY DIFFRACTIONc_scangle_it0.792.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 437 5.3 %
Rwork0.179 7873 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 51094 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.65
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.17

+
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