[English] 日本語
Yorodumi
- PDB-6rnj: TR-SMX closed state structure (0-5ms) of bacteriorhodopsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rnj
TitleTR-SMX closed state structure (0-5ms) of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Retinal / time-resolved crystallography / serial crystallography / SMX
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsWeinert, T. / Skopintsev, P. / James, D. / Kekilli, D. / Furrer, F. / Bruenle, S. / Mous, S. / Nogly, P. / Standfuss, J.
CitationJournal: Science / Year: 2019
Title: Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography.
Authors: Weinert, T. / Skopintsev, P. / James, D. / Dworkowski, F. / Panepucci, E. / Kekilli, D. / Furrer, A. / Brunle, S. / Mous, S. / Ozerov, D. / Nogly, P. / Wang, M. / Standfuss, J.
History
DepositionMay 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3462
Polymers25,0621
Non-polymers2841
Water1448
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0386
Polymers75,1853
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6220 Å2
ΔGint-49 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 62.000, 110.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c

-
Components

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 25061.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 5.6 / Details: 100 mM Na/K Phosphate buffer pH 5.6 30 % PEG 2000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981Y
22981Y
32981Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21
SYNCHROTRONSLS X06SA31
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJul 22, 2018
DECTRIS EIGER X 16M2PIXELJul 22, 2018
DECTRIS EIGER X 16M3PIXELJul 22, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SiSINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
31
Reflection

Entry-ID: 6RNJ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Diffraction-IDNet I/σ(I)CC1/2R split
2.6-38.47673790.1162.0411
2.3-38.510589100257.426.950.990.074
2.1-38.513882100984.9313.30.990.034
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible allNum. unique obsCC1/2R split
2.6-2.9811184
2.3-2.3770.50.922100133460.061.53
2.1-2.1824.61.333100138820.520.86
Serial crystallography sample delivery
IDMethod
1injection
2injection
3injection
Serial crystallography sample delivery injection
IDCarrier solventCrystal conc.DescriptionInjector nozzleInjector temperature (K)Jet diameter (µm)
1LCP13high viscosity injectorglass capillary29850
2LCP13flass capillary50

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
CrystFEL0.7data reduction
CrystFEL0.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6Z

5b6z


Resolution: 2.6→38.47 Å / SU ML: 0.5373 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 44.8015
RfactorNum. reflection% reflection
Rfree0.3012 419 6.22 %
Rwork0.2494 --
obs0.2529 6737 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 8 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271838
X-RAY DIFFRACTIONf_angle_d0.4472510
X-RAY DIFFRACTIONf_chiral_restr0.0347294
X-RAY DIFFRACTIONf_plane_restr0.003306
X-RAY DIFFRACTIONf_dihedral_angle_d9.85721046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.4751270.37191926X-RAY DIFFRACTION83.76
2.98-3.750.3571510.29032092X-RAY DIFFRACTION91.22
3.75-38.480.25391410.21492300X-RAY DIFFRACTION97.33

+
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