[English] 日本語
Yorodumi
- PDB-6qi1: Time resolved structural analysis of the full turnover of an enzy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qi1
TitleTime resolved structural analysis of the full turnover of an enzyme - 12312 ms
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / time-resolved / catalysis / intermediate
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
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.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,2253
Polymers68,1472
Non-polymers781
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-18 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.760, 79.610, 84.430
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fluoroacetate 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


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


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: batch mode
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, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9627 Å / Relative weight: 1
ReflectionResolution: 1.9→82.32 Å / Num. obs: 42453 / % possible obs: 99.9 % / Redundancy: 31.1 % / Net I/σ(I): 2.1
Reflection shellResolution: 1.9→1.94 Å
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.9→20.048 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.99
RfactorNum. reflection% reflection
Rfree0.2588 2087 4.92 %
Rwork0.212 --
obs0.2143 42453 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→20.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 5 448 5135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054887
X-RAY DIFFRACTIONf_angle_d0.7566658
X-RAY DIFFRACTIONf_dihedral_angle_d15.2993957
X-RAY DIFFRACTIONf_chiral_restr0.044683
X-RAY DIFFRACTIONf_plane_restr0.005874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.35291410.28642635X-RAY DIFFRACTION100
1.9442-1.99280.37381250.27892734X-RAY DIFFRACTION100
1.9928-2.04660.30821590.27182626X-RAY DIFFRACTION100
2.0466-2.10680.32551380.26712681X-RAY DIFFRACTION100
2.1068-2.17470.29771170.25762695X-RAY DIFFRACTION100
2.1747-2.25230.34111410.24552679X-RAY DIFFRACTION100
2.2523-2.34240.3281350.24272702X-RAY DIFFRACTION100
2.3424-2.44880.27731380.23372682X-RAY DIFFRACTION100
2.4488-2.57770.25871300.23262716X-RAY DIFFRACTION100
2.5777-2.73880.27641540.2242665X-RAY DIFFRACTION100
2.7388-2.94960.28491270.21342706X-RAY DIFFRACTION100
2.9496-3.24530.27011260.19832689X-RAY DIFFRACTION100
3.2453-3.71240.2111560.18372689X-RAY DIFFRACTION100
3.7124-4.66740.20061350.1672743X-RAY DIFFRACTION100
4.6674-20.04950.21611650.18742724X-RAY DIFFRACTION100

+
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