[English] 日本語
- PDB-6qhs: Time resolved structural analysis of the full turnover of an enzy... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6qhs
TitleTime resolved structural analysis of the full turnover of an enzyme - 564 ms
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / time-resolved / catalysis / intermediate
Function / homology
Function and homology information

haloacetate dehalogenase activity / haloacetate dehalogenase
Similarity search - Function
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
fluoroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
AuthorsSchulz, E.C. / Mehrabi, P. / Pai, E.F. / Miller, D.
CitationJournal: Science / Year: 2019
Title: Time-resolved crystallography reveals allosteric communication aligned with molecular breathing.
Authors: Mehrabi, P. / Schulz, E.C. / Dsouza, R. / Muller-Werkmeister, H.M. / Tellkamp, F. / Miller, R.J.D. / Pai, E.F.
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release

Structure visualization

Structure viewerMolecule:

Downloads & links


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

Theoretical massNumber of molelcules
Total (without water)68,2253

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-18 kcal/mol
Surface area19570 Å2
Unit cell
Length a, b, c (Å)41.330, 78.610, 83.560
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211


#1: Protein Fluoroacetate dehalogenase / Haloacetate dehalogenase

Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-FAH / fluoroacetic acid / Fluoroacetic acid

Mass: 78.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 18-20 % (w/v)) PEG3350, 200 mM CaCl2, and 100 mM Tris-HCl pH 8.5

Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0089 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.72→81.47 Å / Num. obs: 53368 / % possible obs: 95.4 % / Redundancy: 64.1 % / Net I/σ(I): 7.1
Reflection shellResolution: 1.72→1.73 Å
Serial crystallography sample deliveryMethod: fixed target


PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u
Resolution: 1.733→81.464 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.1966 2634 4.94 %
Rwork0.1591 --
obs0.161 53368 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.733→81.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 5 459 5163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155014
X-RAY DIFFRACTIONf_angle_d1.4886865
X-RAY DIFFRACTIONf_dihedral_angle_d14.6155110
X-RAY DIFFRACTIONf_chiral_restr0.075708
X-RAY DIFFRACTIONf_plane_restr0.01906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.733-1.76450.3941000.31791932X-RAY DIFFRACTION73
1.7645-1.79840.29941400.23382743X-RAY DIFFRACTION100
1.7984-1.83510.25491310.18232675X-RAY DIFFRACTION100
1.8351-1.8750.22231400.16662724X-RAY DIFFRACTION100
1.875-1.91860.2191050.1552697X-RAY DIFFRACTION100
1.9186-1.96660.22341240.15522761X-RAY DIFFRACTION100
1.9666-2.01980.19841510.15442657X-RAY DIFFRACTION100
2.0198-2.07920.19821310.14992711X-RAY DIFFRACTION100
2.0792-2.14640.20741560.14922678X-RAY DIFFRACTION100
2.1464-2.22310.18671480.14142699X-RAY DIFFRACTION100
2.2231-2.31210.20131210.14952738X-RAY DIFFRACTION100
2.3121-2.41730.20591460.14772691X-RAY DIFFRACTION100
2.4173-2.54480.21251430.1522716X-RAY DIFFRACTION100
2.5448-2.70420.21281600.15622681X-RAY DIFFRACTION100
2.7042-2.9130.19961350.15142705X-RAY DIFFRACTION100
2.913-3.20620.20011520.15562705X-RAY DIFFRACTION100
3.2062-3.67010.17041560.14742709X-RAY DIFFRACTION100
3.6701-4.62390.16461300.152763X-RAY DIFFRACTION100
4.6239-81.55420.17871650.17942749X-RAY DIFFRACTION100

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