[English] 日本語
Yorodumi
- PDB-8b6r: X-ray structure of the haloalkane dehalogenase HaloTag7 labeled w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b6r
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 labeled with a chloroalkane Cyanine3 fluorophore substrate
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / fluorophore / cyanine 3 / Cy3
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PJI / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTarnawski, M. / Hellweg, L. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A general method for the development of multicolor biosensors with large dynamic ranges.
Authors: Hellweg, L. / Edenhofer, A. / Barck, L. / Huppertz, M.C. / Frei, M.S. / Tarnawski, M. / Bergner, A. / Koch, B. / Johnsson, K. / Hiblot, J.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3178
Polymers33,2261
Non-polymers1,0917
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.560, 112.560, 44.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Haloalkane dehalogenase


Mass: 33225.980 Da / Num. of mol.: 1
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

-
Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-PJI / ~{N}-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-6-[3,3-dimethyl-2-[(~{E})-3-(1,3,3-trimethylindol-2-ylidene)prop-1-enyl]indol-1-ium-1-yl]hexanamide


Mass: 663.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H57ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M magnesium acetate, 19% (m/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999884 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999884 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 46121 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.21
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 7965 / CC1/2: 0.902 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.5→41.25 Å / SU ML: 0.181 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.6079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 2306 5 %
Rwork0.162 43814 -
obs0.1635 46120 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 72 297 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01272516
X-RAY DIFFRACTIONf_angle_d1.22863438
X-RAY DIFFRACTIONf_chiral_restr0.0807359
X-RAY DIFFRACTIONf_plane_restr0.0109466
X-RAY DIFFRACTIONf_dihedral_angle_d9.2195375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.39371420.3542709X-RAY DIFFRACTION99.79
1.53-1.570.28931410.2322674X-RAY DIFFRACTION99.93
1.57-1.610.23831410.19192689X-RAY DIFFRACTION99.89
1.61-1.650.23231430.18722705X-RAY DIFFRACTION99.89
1.65-1.70.24891420.1882705X-RAY DIFFRACTION99.93
1.7-1.750.23231410.17382686X-RAY DIFFRACTION100
1.75-1.820.20311430.16192704X-RAY DIFFRACTION99.96
1.82-1.890.20851430.14342719X-RAY DIFFRACTION99.86
1.89-1.980.16331430.15072714X-RAY DIFFRACTION100
1.98-2.080.17381430.1552728X-RAY DIFFRACTION99.93
2.08-2.210.19311450.15272741X-RAY DIFFRACTION100
2.21-2.380.1721430.15282730X-RAY DIFFRACTION100
2.38-2.620.16551460.15932770X-RAY DIFFRACTION99.93
2.62-30.17551460.15982771X-RAY DIFFRACTION99.93
3-3.780.18171480.15232808X-RAY DIFFRACTION99.9
3.78-41.250.18121560.15172961X-RAY DIFFRACTION99.87

+
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