[English] 日本語
Yorodumi
- PDB-6zvv: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W LAB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zvv
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / HALOTAG7 / SELF-LABELING PROTEIN / FLUOROPHORE / TETRAMETHYLRHODAMINE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
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
Chem-OEH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
CitationJournal: To Be Published
Title: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
Authors: Tarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,17515
Polymers133,2604
Non-polymers2,91511
Water24,7351373
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0804
Polymers33,3151
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0284
Polymers33,3151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9883
Polymers33,3151
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0804
Polymers33,3151
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.260, 53.030, 163.210
Angle α, β, γ (deg.)90.000, 93.746, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Haloalkane dehalogenase


Mass: 33315.074 Da / Num. of mol.: 4
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, 1384 molecules

#2: Chemical
ChemComp-OEH / [9-[2-carboxy-5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 637.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1373 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate, 20% (m/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 230075 / % possible obs: 97.4 % / Redundancy: 3.16 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 40203 / CC1/2: 0.82 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.4→42.29 Å / SU ML: 0.1543 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.1738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 11503 5 %
Rwork0.1993 218539 -
obs0.2006 230042 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.71 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9401 0 193 1373 10967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619949
X-RAY DIFFRACTIONf_angle_d0.883613606
X-RAY DIFFRACTIONf_chiral_restr0.08121413
X-RAY DIFFRACTIONf_plane_restr0.00661904
X-RAY DIFFRACTIONf_dihedral_angle_d8.63024849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.27163110.24715912X-RAY DIFFRACTION79.46
1.42-1.430.26243360.24156383X-RAY DIFFRACTION85.84
1.43-1.450.27533570.23216783X-RAY DIFFRACTION91.99
1.45-1.470.26363810.22287238X-RAY DIFFRACTION96.54
1.47-1.490.24863850.21127322X-RAY DIFFRACTION99.41
1.49-1.510.24783930.20527454X-RAY DIFFRACTION99.81
1.51-1.530.23753910.19517435X-RAY DIFFRACTION99.73
1.53-1.550.22133900.19627417X-RAY DIFFRACTION99.63
1.55-1.580.24563890.20167380X-RAY DIFFRACTION99.65
1.58-1.60.23953920.19757448X-RAY DIFFRACTION99.56
1.6-1.630.2163910.19627441X-RAY DIFFRACTION99.66
1.63-1.660.24383890.19587383X-RAY DIFFRACTION99.34
1.66-1.690.22793880.19437374X-RAY DIFFRACTION99.44
1.69-1.730.23373910.1947416X-RAY DIFFRACTION99.34
1.73-1.760.22713900.19647422X-RAY DIFFRACTION99.2
1.76-1.80.22563850.19697318X-RAY DIFFRACTION98.81
1.8-1.850.25243890.19977385X-RAY DIFFRACTION98.76
1.85-1.90.22483900.19817409X-RAY DIFFRACTION98.8
1.9-1.960.21313900.19967405X-RAY DIFFRACTION98.96
1.96-2.020.23493850.20257319X-RAY DIFFRACTION98.64
2.02-2.090.2153880.19797366X-RAY DIFFRACTION98.4
2.09-2.170.22093860.20047335X-RAY DIFFRACTION98.61
2.17-2.270.24223880.19837389X-RAY DIFFRACTION98.48
2.27-2.390.22253860.19987338X-RAY DIFFRACTION97.93
2.39-2.540.21793840.19917295X-RAY DIFFRACTION97.03
2.54-2.740.23013880.20867362X-RAY DIFFRACTION98.08
2.74-3.020.22393890.20357391X-RAY DIFFRACTION98.31
3.02-3.450.21133890.19867401X-RAY DIFFRACTION98.04
3.45-4.350.22093930.18987450X-RAY DIFFRACTION97.83
4.35-42.290.20563990.19297568X-RAY DIFFRACTION97.21

+
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