[English] 日本語
Yorodumi
- PDB-7zna: Crystal structure of the light-driven inward proton pump xenorhod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zna
TitleCrystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 5.2 in the presence of sodium at 100K
Componentsxenorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle
Function / homologyEICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION
Function and homology information
Biological speciesBacillus coahuilensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalev, K. / Tsybrov, F. / Alekseev, A. / Bourenkov, G. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Mechanisms of inward transmembrane proton translocation.
Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / ...Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / Chizhov, I. / Royant, A. / Kuzmin, A. / Gushchin, I. / Rosselli, R. / Rodriguez-Valera, F. / Ilyinskiy, N. / Rogachev, A. / Borshchevskiy, V. / Schneider, T.R. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 26, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: xenorhodopsin
B: xenorhodopsin
C: xenorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,15774
Polymers77,1773
Non-polymers18,98071
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31970 Å2
ΔGint116 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.570, 109.590, 119.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: FME / Beg label comp-ID: FME / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1 - 2231 - 223
21GLNGLNBB1 - 2231 - 223
12SERSERAA1 - 2241 - 224
22SERSERCC1 - 2241 - 224
13HISHISBB1 - 2221 - 222
23HISHISCC1 - 2221 - 222

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein xenorhodopsin


Mass: 25725.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coahuilensis (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 6 types, 357 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C20H42
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.8 M Na/K-Pi pH 8.2 crystals soaked in 1.2 M Na/K-Pi pH 5.2 before harvesting

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→49.817 Å / Num. obs: 65268 / % possible obs: 94.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.916 Å / Rmerge(I) obs: 3.376 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3262 / CC1/2: 0.316

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIO

1xio


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.791 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 3194 4.9 %RANDOM
Rwork0.1966 ---
obs0.1982 62007 77.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.58 Å2 / Biso mean: 32.347 Å2 / Biso min: 13.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.09 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 733 289 6279
Biso mean--57.93 45.73 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136183
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156750
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.6488176
X-RAY DIFFRACTIONr_angle_other_deg1.1141.54415517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.865690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.87718.899218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54715848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.821519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026253
X-RAY DIFFRACTIONr_gen_planes_other00.021309
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77460.08
12B77460.08
21A77060.09
22C77060.09
31B76830.07
32C76830.07
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 63 -
Rwork0.335 953 -
all-1016 -
obs--16.66 %

+
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