[English] 日本語
Yorodumi
- PDB-1f4z: BACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f4z
TitleBACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT AT 1.8 ANGSTROM RESOLUTION
ComponentsBACTERIORHODOPSIN
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / ION PUMP / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / ION TRANSPORT / MEROHEDRAL TWINNING / E204Q mutant M state / photocycle intermediate
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
Chem-LI1 / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsLuecke, H. / Schobert, B. / Cartailler, J.P. / Richter, H.T. / Rosengarth, A. / Needleman, R. / Lanyi, J.K.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin.
Authors: Luecke, H. / Schobert, B. / Cartailler, J.P. / Richter, H.T. / Rosengarth, A. / Needleman, R. / Lanyi, J.K.
History
DepositionJun 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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)33,83416
Polymers24,8601
Non-polymers8,97415
Water45025
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,50348
Polymers74,5813
Non-polymers26,92245
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 area24790 Å2
ΔGint-225 kcal/mol
Surface area27990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.631, 60.631, 108.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein BACTERIORHODOPSIN / BR


Mass: 24860.438 Da / Num. of mol.: 1 / Mutation: E204Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Production host: Halobacterium salinarum (Halophile) / 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-SQU / 2,10,23-TRIMETHYL-TETRACOSANE / LIPID FRAGMENT


Mass: 380.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H56
#4: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 295 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.6, Cubic lipid phase, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-70 %(w/v)lipids11
22.5-4.5 mg/mlBR11
30.7-4.0 Msodium potassium phosphate11
41.5-3.75 %MPD11
50.36-0.48 %OG11

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-211
SYNCHROTRONESRF ID1321
SYNCHROTRONSPring-8 BL41XU31
Detector
TypeIDDetectorDate
ADSC QUANTUM1CCDJan 5, 2000
MAR-CCD2CCDFeb 17, 2000
MAR-CCD3CCDMar 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 214773 / Num. obs: 21451 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 28.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.3 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 214773
Reflection shell
*PLUS
% possible obs: 95.1 %

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: ISOMORPHOUS WITH 1C3W

1c3w


Resolution: 1.8→12 Å / Num. parameters: 8252 / Num. restraintsaints: 8198 / Cross valid method: 5% / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Twin ratio is 58:42, R-factor (F>4sig)=0.131, R-free (F>4sig)=0.190
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1039 -5% of the data was omitted via thin-resolution shell selection
Rwork0.142 ---
all-20778 --
obs-20778 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 330 25 2075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.142 / Rfactor obs: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.024

+
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