[English] 日本語
Yorodumi
- PDB-7o8g: NmHR light state structure at 10 ps after photoexcitation determi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o8g
TitleNmHR light state structure at 10 ps after photoexcitation determined by serial femtosecond crystallography (with extrapolated, dark and light dataset)
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride pump / rhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. ...Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Bruenle, S. / Casadei, C. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPZ00P3_174169 Switzerland
CitationJournal: Science / Year: 2022
Title: Dynamics and mechanism of a light-driven chloride pump.
Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / ...Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G.F.X. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P.
History
DepositionApr 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 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: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,43310
Polymers32,9131
Non-polymers2,5199
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-12 kcal/mol
Surface area11900 Å2
Unit cell
Length a, b, c (Å)104.480, 51.180, 78.330
Angle α, β, γ (deg.)90.000, 131.780, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Chloride pumping rhodopsin


Mass: 32913.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: W8VZW3

-
Non-polymers , 5 types, 76 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 50 mM sodium acetate (pH 4.5), 150 mM MgCl2, 100 mM NaCl, 34% PEG400

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→13.5 Å / Num. obs: 55801 / % possible obs: 100 % / Redundancy: 166 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.2
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 5183 / CC1/2: 0.34
Serial crystallography sample deliveryMethod: injection

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrystFELv0.8.0data reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
CrystFELv0.8.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 1.9→13.45 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 38.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3355 1197 5.12 %
Rwork0.2867 22184 -
obs0.2891 23381 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.93 Å2 / Biso mean: 24.585 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 1.9→13.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 162 67 2286
Biso mean--28.42 27.28 -
Num. residues----262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.980.49851310.44362178230986
1.98-2.070.37291490.38762295244491
2.07-2.170.37941330.34432405253894
2.17-2.310.37771550.31622432258796
2.31-2.490.37891250.30142492261798
2.49-2.740.34381170.27562582269999
2.74-3.130.30791350.26832565270099
3.13-3.920.29471230.24942601272499
3.92-13.450.29941290.26522634276399

+
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