[English] 日本語
Yorodumi
- PDB-1c8s: BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c8s
TitleBACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE
ComponentsBACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
KeywordsION TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / D96N M INTERMEDIATE / MEROHEDRAL TWINNING
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / 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 / ISOMORPHOUS / Resolution: 2 Å
AuthorsLuecke, H.
Citation
Journal: Science / Year: 1999
Title: Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution
Authors: Luecke, H. / Schobert, B. / Richter, H.-T. / Cartailler, J.-P. / Lanyi, J.K.
#2: Journal: Science / Year: 1998
Title: Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution
Authors: Luecke, H. / Richter, H.-T. / Lanyi, J.K.
History
DepositionJul 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,06514
Polymers21,3691
Non-polymers7,69613
Water25214
1
A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN ("M" STATE INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19542
Polymers64,1083
Non-polymers23,08739
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 area26710 Å2
ΔGint-233 kcal/mol
Surface area25350 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 ("M" STATE INTERMEDIATE)


Mass: 21369.309 Da / Num. of mol.: 1 / Mutation: D96N
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 301 (C15) DIETHER LIPID BILAYER
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.: 11 / 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.: 14 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 296 K / Method: cubic lipid phase / pH: 5.6
Details: MO:WATER:PHOSPHATE, pH 5.6, CUBIC LIPID PHASE, temperature 296K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: other / Details: Gabriele, R., (1998) J. Struct. Biol., 121, 82.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 mg/mlprotein11
21 Msodium potassium Pi11
32.5 %MPD11

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211
SYNCHROTRONESRF ID1321
Detector
TypeIDDetector
ADSC1CCD
MAR CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 14622 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Num. measured all: 110517
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.33

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOMORPHOUS
Starting model: PDB ENTRY 1C3W

1c3w


Resolution: 2→12 Å / Num. parameters: 7288 / Num. restraintsaints: 7357 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MEROHEDRAL TWINNING RATIO OF 53:47
RfactorNum. reflection% reflectionSelection details
Rfree0.219 734 5 %THIN RESOLUTION SHELLS
all0.173 14622 --
obs0.172 -95 %-
Solvent computationSolvent model: SHELXL-97 SWAT, BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 297 14 1821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.261
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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