[English] 日本語
Yorodumi
- PDB-9i6h: Room temperature structure of KR2 rhodopsin in pentameric form at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i6h
TitleRoom temperature structure of KR2 rhodopsin in pentameric form at 95% relative humidity
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / Sodium pump
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Melo, D. / de Wijn, R. / Bean, R. / Round, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.
Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, ...Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, L. / Bean, R. / Round, A.
History
DepositionJan 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium pumping rhodopsin
B: Sodium pumping rhodopsin
C: Sodium pumping rhodopsin
D: Sodium pumping rhodopsin
E: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,87490
Polymers154,0385
Non-polymers25,83685
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35940 Å2
ΔGint-199 kcal/mol
Surface area43040 Å2
Unit cell
Length a, b, c (Å)136.100, 240.900, 138.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 30807.639 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dokdonia eikasta (bacteria) / Gene: NaR / Production host: Escherichia coli (E. coli) / References: UniProt: N0DKS8

-
Non-polymers , 5 types, 289 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C20H42
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 297 K / Method: lipidic cubic phase / pH: 8 / Details: 3.2M sodium malonate pH 8.0 / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 297 K / Ambient temp details: Room temperature / 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 4M / Detector: PIXEL / Date: Jul 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→69.25 Å / Num. obs: 45854 / % possible obs: 100 % / Redundancy: 89 % / Biso Wilson estimate: 65.37 Å2 / R split: 0.3646 / Net I/σ(I): 2.65
Reflection shellResolution: 3→3.11 Å / Redundancy: 61.4 % / Num. unique obs: 4499 / R split: 1.3075 / % possible all: 100

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
CrystFEL0.10.1data reduction
CrystFEL0.10.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→69.25 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2033 2283 4.98 %
Rwork0.1708 43571 -
obs0.1725 45854 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.41 Å2
Refinement stepCycle: LAST / Resolution: 3→69.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10636 0 1099 204 11939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002811945
X-RAY DIFFRACTIONf_angle_d0.531515861
X-RAY DIFFRACTIONf_chiral_restr0.04031702
X-RAY DIFFRACTIONf_plane_restr0.0051868
X-RAY DIFFRACTIONf_dihedral_angle_d15.80954347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.30471300.23162708X-RAY DIFFRACTION99.58
3.07-3.140.24151570.20032646X-RAY DIFFRACTION99.96
3.14-3.210.24851510.19732702X-RAY DIFFRACTION99.93
3.22-3.30.26211300.18412695X-RAY DIFFRACTION100
3.3-3.40.19531430.17312694X-RAY DIFFRACTION100
3.4-3.510.23041280.16882706X-RAY DIFFRACTION100
3.51-3.630.19841560.15992704X-RAY DIFFRACTION100
3.63-3.780.2151470.16172688X-RAY DIFFRACTION100
3.78-3.950.17791320.15392719X-RAY DIFFRACTION100
3.95-4.160.17351400.13962719X-RAY DIFFRACTION100
4.16-4.420.16791540.14212703X-RAY DIFFRACTION100
4.42-4.760.18991420.14962736X-RAY DIFFRACTION100
4.76-5.240.19341400.15822738X-RAY DIFFRACTION100
5.24-60.20131470.18612741X-RAY DIFFRACTION100
6-7.560.21321450.19322787X-RAY DIFFRACTION100
7.56-69.250.20761410.1972885X-RAY DIFFRACTION99.51

+
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