[English] 日本語
Yorodumi
- PDB-7zou: Crystal structure of Synechocystis halorhodopsin (SyHR), Cl-pumpi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zou
TitleCrystal structure of Synechocystis halorhodopsin (SyHR), Cl-pumping mode, ground state
ComponentsSynechocystis halorhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / syhr / trapping / cryo / cryotrapping / o-state / k-state / sulfate / chloride / pump / anion / photocycle / ion transport
Function / homologyEICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciesSynechocystis sp. PCC 7509 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKovalev, K. / Bukhdruker, S. / Astashkin, R. / Vaganova, S. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
Ministry of Science and Higher Education of the Russian Federation075-00337-20-03/FSMG-2020-0003 Russian Federation
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-10-LABX-49-01 France
Russian Science Foundation16-15-00242 Russian Federation
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into light-driven anion pumping in cyanobacteria.
Authors: Astashkin, R. / Kovalev, K. / Bukhdruker, S. / Vaganova, S. / Kuzmin, A. / Alekseev, A. / Balandin, T. / Zabelskii, D. / Gushchin, I. / Royant, A. / Volkov, D. / Bourenkov, G. / Koonin, E. / ...Authors: Astashkin, R. / Kovalev, K. / Bukhdruker, S. / Vaganova, S. / Kuzmin, A. / Alekseev, A. / Balandin, T. / Zabelskii, D. / Gushchin, I. / Royant, A. / Volkov, D. / Bourenkov, G. / Koonin, E. / Engelhard, M. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,22322
Polymers26,4631
Non-polymers5,76021
Water2,252125
1
A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,66866
Polymers79,3893
Non-polymers17,27963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area22200 Å2
ΔGint-110 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.980, 61.980, 109.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Synechocystis halorhodopsin


Mass: 26463.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MAQIWLWIGVIGMALGSIFFGIGAHNAKNERWKILFTINFFICAIATGLYLSMALGQGRSVIAGRPTVWV RYITWFLSTPLLILDLTFLGKTSLPITASLLGANAYMIATGFVATISADRTIGHIWYVVSCFAFLATVYL ...Details: MAQIWLWIGVIGMALGSIFFGIGAHNAKNERWKILFTINFFICAIATGLYLSMALGQGRSVIAGRPTVWV RYITWFLSTPLLILDLTFLGKTSLPITASLLGANAYMIATGFVATISADRTIGHIWYVVSCFAFLATVYL LVNQYRKQAERNYPQAKKVFRKLLSVHLVLWTLYPIVWLLGNTGFNAVNQGTETMFYTILDITSKVGFGF LSLNSMHTLEKNTESVSSYESSTI
Source: (gene. exp.) Synechocystis sp. PCC 7509 (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#4: 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
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1.6 M Ammonium Phosphate

-
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: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.58→53.68 Å / Num. obs: 33368 / % possible obs: 96.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 18.07 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.059 / Net I/σ(I): 8
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 1667 / CC1/2: 0.225 / Rpim(I) all: 0.993

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYJ

4hyj


Resolution: 1.58→19.95 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 1712 5.14 %
Rwork0.1735 31619 -
obs0.175 33331 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.81 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 239 125 2154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052203
X-RAY DIFFRACTIONf_angle_d0.83732933
X-RAY DIFFRACTIONf_chiral_restr0.0513312
X-RAY DIFFRACTIONf_plane_restr0.0052344
X-RAY DIFFRACTIONf_dihedral_angle_d16.1431858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.36171070.32792015X-RAY DIFFRACTION76.03
1.62-1.670.28471320.27772489X-RAY DIFFRACTION91.8
1.68-1.730.28631220.25152558X-RAY DIFFRACTION95.95
1.73-1.80.27331320.22562655X-RAY DIFFRACTION98.2
1.8-1.890.22381560.20622680X-RAY DIFFRACTION99.89
1.89-1.990.25371420.19782675X-RAY DIFFRACTION100
1.99-2.110.21611380.15422730X-RAY DIFFRACTION100
2.11-2.270.14541190.14462739X-RAY DIFFRACTION100
2.27-2.50.17751490.14992714X-RAY DIFFRACTION100
2.5-2.860.1931820.14572716X-RAY DIFFRACTION100
2.86-3.60.18311610.15562771X-RAY DIFFRACTION99.97
3.6-19.950.18591720.16972877X-RAY DIFFRACTION99.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.238594483572-0.134302002552-0.1352880195270.2404137794720.08606000127620.0893217695610.02188072151770.04394903477120.108467153953-0.06385574084780.034028365133-0.00828485695738-0.122360431080.01112885247240.000581286064710.167806211383-0.006312207186760.004326055345060.1535699666180.004760993266450.184357875283-17.2125353461-1.74876265095-27.9016910177
20.06258004557260.06197998321160.07332547726570.130729067890.09814027295010.0862387094938-0.005723519989180.0157492461774-0.01608584264320.01425992537190.03516128910040.01962193602270.0729901867301-0.05428778572632.68044122103E-50.1623431937590.001685945533740.003760214428780.143304786410.008783464411420.142090923738-18.5189490167-14.5020135667-20.7384605626
30.4117159141050.05312479934850.253703525540.361785481418-0.208776326920.345243085602-0.007431061491720.0619806092069-0.0439750946706-0.06012736224390.0161064543194-0.04812098913430.08728020552510.09349444202413.9551419023E-50.144110223249-0.006268508543670.008284697459280.15129074811-0.009343684576010.142863573372-10.9566364725-22.4911220318-26.1123831338
40.195376109920.0533414082192-0.006345566019770.3647072348570.03082263518170.0274655735391-0.003780631280120.03083206804930.0594593699104-0.0950239551593-0.0223071699084-0.0589099598275-0.04618760207890.0274181705477-1.97429244844E-50.1677264499-0.004549379513350.01297451943120.176002685270.01377926655220.169443809225-9.23840376584-8.61008770127-29.9705888553
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 54 )1 - 541 - 54
22chain 'A' and (resid 55 through 93 )55 - 9355 - 93
33chain 'A' and (resid 94 through 189 )94 - 18994 - 189
44chain 'A' and (resid 190 through 225 )190 - 225190 - 225

+
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