[English] 日本語
Yorodumi
- PDB-8b6p: X-ray structure of the haloalkane dehalogenase HaloTag7 circular ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b6p
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 154-156 (cpHaloTag7_154-156)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTarnawski, M. / Johnsson, K. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2024
Title: Recording physiological history of cells with chemical labeling.
Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, ...Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, C. / Fenk, L.M. / Baier, H. / Hiblot, J. / Johnsson, K.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6174
Polymers68,5462
Non-polymers712
Water12,250680
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers34,2731
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers34,2731
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.870, 94.660, 100.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Haloalkane dehalogenase


Mass: 34272.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Bicine pH 9.0, 1.6 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 251839 / % possible obs: 95.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 8.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.68
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 8.49 / Num. unique obs: 54597 / CC1/2: 0.965 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2X

5y2x


Resolution: 1.1→42.79 Å / SU ML: 0.0651 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 11.6472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.149 12591 5 %
Rwork0.137 239241 -
obs0.1376 251832 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.99 Å2
Refinement stepCycle: LAST / Resolution: 1.1→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 2 680 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00984897
X-RAY DIFFRACTIONf_angle_d1.16546696
X-RAY DIFFRACTIONf_chiral_restr0.098707
X-RAY DIFFRACTIONf_plane_restr0.0134883
X-RAY DIFFRACTIONf_dihedral_angle_d5.6112644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.14213360.12516396X-RAY DIFFRACTION77.13
1.11-1.130.1373830.1157277X-RAY DIFFRACTION87.66
1.13-1.140.12994030.11157656X-RAY DIFFRACTION92.93
1.14-1.150.13484110.10887808X-RAY DIFFRACTION93.99
1.15-1.170.14994140.11267861X-RAY DIFFRACTION94.44
1.17-1.180.14064130.11057845X-RAY DIFFRACTION94.85
1.18-1.20.13674160.11367904X-RAY DIFFRACTION95.13
1.2-1.220.13784150.11227895X-RAY DIFFRACTION95.3
1.22-1.240.13654140.11197864X-RAY DIFFRACTION95.13
1.24-1.260.13184200.11057980X-RAY DIFFRACTION95.53
1.26-1.280.12924190.11017957X-RAY DIFFRACTION96
1.28-1.30.13114230.11218027X-RAY DIFFRACTION96.31
1.3-1.330.12874200.10947990X-RAY DIFFRACTION96.19
1.33-1.360.1344210.11358001X-RAY DIFFRACTION96.34
1.36-1.390.14594220.11558012X-RAY DIFFRACTION96.32
1.39-1.420.144210.11367995X-RAY DIFFRACTION95.9
1.42-1.450.14114240.11748064X-RAY DIFFRACTION96.55
1.45-1.490.13534250.11438073X-RAY DIFFRACTION96.99
1.49-1.540.13414270.11138110X-RAY DIFFRACTION97.03
1.54-1.590.1294270.11268110X-RAY DIFFRACTION97.14
1.59-1.640.13114280.1148138X-RAY DIFFRACTION97.2
1.64-1.710.14414270.12268112X-RAY DIFFRACTION97.08
1.71-1.790.13324260.12698101X-RAY DIFFRACTION96.49
1.79-1.880.14654310.13898184X-RAY DIFFRACTION97.8
1.88-20.15334320.14288216X-RAY DIFFRACTION97.75
2-2.150.14574330.14288210X-RAY DIFFRACTION97.47
2.15-2.370.14784330.14878227X-RAY DIFFRACTION97.1
2.37-2.710.17814330.16238227X-RAY DIFFRACTION97.14
2.71-3.420.17484410.17078398X-RAY DIFFRACTION98.13
3.42-42.790.15714530.15818603X-RAY DIFFRACTION97.37

+
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