[English] 日本語
Yorodumi
- PDB-9f9c: Laser excitation effects on BR: Reprocessed Extrapolated 16 ns Li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f9c
TitleLaser excitation effects on BR: Reprocessed Extrapolated 16 ns Light dataset recorded at 0.04 GW/cm2 from Nango et al.
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Bacteriorhodospin / Membrane / RETINAL / TIME-RESOLVED CRYSTALLOGRAPHY / SERIAL CRYSTALLOGRAPHY / Laser excitation
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
Similarity search - Domain/homology
Chem-LI1 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBertrand, Q. / Weinert, T. / Standfuss, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Innosuisse42711.1 IP-LSEuropean Union
CitationJournal: Nat Commun / Year: 2024
Title: Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate.
Authors: Bertrand, Q. / Nogly, P. / Nango, E. / Kekilli, D. / Khusainov, G. / Furrer, A. / James, D. / Dworkowski, F. / Skopintsev, P. / Mous, S. / Martiel, I. / Borjesson, P. / Ortolani, G. / Huang, ...Authors: Bertrand, Q. / Nogly, P. / Nango, E. / Kekilli, D. / Khusainov, G. / Furrer, A. / James, D. / Dworkowski, F. / Skopintsev, P. / Mous, S. / Martiel, I. / Borjesson, P. / Ortolani, G. / Huang, C.Y. / Kepa, M. / Ozerov, D. / Brunle, S. / Panneels, V. / Tanaka, T. / Tanaka, R. / Tono, K. / Owada, S. / Johnson, P.J.M. / Nass, K. / Knopp, G. / Cirelli, C. / Milne, C. / Schertler, G. / Iwata, S. / Neutze, R. / Weinert, T. / Standfuss, J.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28119
Polymers25,2621
Non-polymers10,01918
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-58 kcal/mol
Surface area12510 Å2
Unit cell
Length a, b, c (Å)62.950, 62.950, 111.700
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: 25261.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945
#2: Chemical
ChemComp-LI1 / 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL / LIPID FRAGMENT


Mass: 639.130 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C42H86O3
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-RET / RETINAL / BR / Bacterioopsin / BO


Mass: 284.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.1M Na/K phosphate pH5.4, 30% PEG 2000

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.63 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.63 Å / Relative weight: 1
ReflectionResolution: 1.95→38.92 Å / Num. obs: 18140 / % possible obs: 100 % / Redundancy: 369 % / CC star: 0.996 / R split: 0.0632 / Net I/σ(I): 12.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 64 % / Mean I/σ(I) obs: 1.111 / Num. unique obs: 1820 / CC star: 0.825 / R split: 0.7803 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15.74 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1653 10.01 %
Rwork0.212 --
obs0.2167 16509 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→15.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 245 35 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022122
X-RAY DIFFRACTIONf_angle_d0.7922821
X-RAY DIFFRACTIONf_dihedral_angle_d15.023813
X-RAY DIFFRACTIONf_chiral_restr0.035309
X-RAY DIFFRACTIONf_plane_restr0.011331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.66151250.571143X-RAY DIFFRACTION90
2.06-2.120.4751320.46211189X-RAY DIFFRACTION96
2.13-2.20.351420.32541237X-RAY DIFFRACTION97
2.2-2.290.3181360.27251242X-RAY DIFFRACTION98
2.29-2.390.28261370.2161242X-RAY DIFFRACTION98
2.39-2.520.20591410.19971259X-RAY DIFFRACTION98
2.52-2.680.26561310.17851236X-RAY DIFFRACTION98
2.68-2.880.23321400.17031243X-RAY DIFFRACTION98
2.88-3.170.21341400.16581255X-RAY DIFFRACTION99
3.17-3.620.2121430.16671250X-RAY DIFFRACTION99
3.62-4.540.2071440.15431281X-RAY DIFFRACTION100
4.55-15.740.21511420.18361279X-RAY DIFFRACTION99
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)
13.48130.502-1.9653.4646-2.08866.5917-0.0095-0.0704-0.25860.0984-0.1376-0.3250.43130.55560.06020.12890.0311-0.01920.10490.0090.255422.460126.513733.6758
21.3374-0.3262-0.22481.84780.56620.5411-0.0241-0.0756-0.0203-0.04640.02630.01910.03070.0067-0.0060.1149-0.0184-0.02110.13270.02090.185911.98437.98434.7086
34.0753-0.23591.41712.5578-0.98446.39170.0509-0.07240.20.1455-0.0553-0.2694-0.26230.06560.06620.136-0.0291-0.00070.06110.01460.179112.544753.243131.2373
48.2842-7.39716.60466.8585-5.47545.9985-0.8012-1.08380.18761.20160.81970.5851-1.1589-0.4108-0.07650.5708-0.0290.08340.7785-0.08050.497317.722846.951357.932
51.0107-0.02010.10821.1883-0.44222.25960.0385-0.020.08240.081-0.0385-0.241-0.13230.3141-0.01910.1166-0.036-0.0530.17070.01260.203723.020742.365235.173
62.97930.99720.33583.3388-2.7352.7358-0.2818-0.6207-0.39020.4261-0.2926-0.47451.32931.32940.67860.55530.0503-0.0940.49950.10250.270621.574630.951759.8706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 234 )

+
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