[English] 日本語
Yorodumi
- PDB-6rmk: Bacteriorhodopsin, dark state, cell 2, refined using the same pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rmk
TitleBacteriorhodopsin, dark state, cell 2, refined using the same protocol as sub-ps time delays
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / proton pump / time-resolved crystallography / free-electron laser
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. ...Nass Kovacs, G. / Colletier, J.-P. / Gruenbein, M.L. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2019
Title: Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.
Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / ...Authors: Nass Kovacs, G. / Colletier, J.P. / Grunbein, M.L. / Yang, Y. / Stensitzki, T. / Batyuk, A. / Carbajo, S. / Doak, R.B. / Ehrenberg, D. / Foucar, L. / Gasper, R. / Gorel, A. / Hilpert, M. / Kloos, M. / Koglin, J.E. / Reinstein, J. / Roome, C.M. / Schlesinger, R. / Seaberg, M. / Shoeman, R.L. / Stricker, M. / Boutet, S. / Haacke, S. / Heberle, J. / Heyne, K. / Domratcheva, T. / Barends, T.R.M. / Schlichting, I.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5882
Polymers25,3041
Non-polymers2841
Water64936
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7656
Polymers75,9123
Non-polymers8533
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 area6420 Å2
ΔGint-52 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 62.100, 110.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 25303.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 / Variant: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 32% (W/V) PEG 2000, 0.1 M K2HPO4 /NAH2PO4, IN HAMILTON SYRINGES, PH 5.6, LIPIDIC CUBIC PHASE,

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.26 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.8→20.444 Å / Num. obs: 22403 / % possible obs: 100 % / Redundancy: 476 % / R split: 0.154 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 1140

-
Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6V

5b6v


Resolution: 1.8→20.441 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2492 1137 5.08 %
Rwork0.2435 --
obs0.2439 22360 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 20 36 1843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061855
X-RAY DIFFRACTIONf_angle_d0.9332533
X-RAY DIFFRACTIONf_dihedral_angle_d15.5811051
X-RAY DIFFRACTIONf_chiral_restr0.048298
X-RAY DIFFRACTIONf_plane_restr0.01304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.43491490.39842660X-RAY DIFFRACTION100
1.8819-1.98110.34681440.34742637X-RAY DIFFRACTION100
1.9811-2.10510.29741430.29232620X-RAY DIFFRACTION100
2.1051-2.26740.24721410.26232640X-RAY DIFFRACTION100
2.2674-2.49520.25081340.24992674X-RAY DIFFRACTION100
2.4952-2.85540.22731300.21992645X-RAY DIFFRACTION100
2.8554-3.59440.20881420.20242665X-RAY DIFFRACTION100
3.5944-20.44270.24911540.23942682X-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