[English] 日本語
Yorodumi
- PDB-1brr: X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1brr
TitleX-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX
ComponentsPROTEIN (BACTERIORHODOPSIN)
KeywordsPROTON TRANSPORT / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA
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
3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL / beta-D-glucopyranose / N-OCTANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEssen, L.-O. / Siegert, R. / Oesterhelt, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex
Authors: Essen, L. / Siegert, R. / Lehmann, W.D. / Oesterhelt, D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Orthorhombic Crystal Form of Bacteriorhodopsin Nucleated on Benzamidine Diffracting to 3.6 Angstrom Resolution
Authors: Schertler, G.F.X. / Bartunik, H.D. / Michel, H. / Oesterhelt, D.
History
DepositionJul 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_poly / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (BACTERIORHODOPSIN)
B: PROTEIN (BACTERIORHODOPSIN)
C: PROTEIN (BACTERIORHODOPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,79923
Polymers80,2213
Non-polymers5,57820
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18020 Å2
ΔGint-143 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.520, 105.960, 80.190
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
22
33
/ NCS ensembles :
ID
2
3

NCS oper:
IDCodeMatrixVector
1given(0.4482, -0.554, 0.7016), (0.4964, -0.4985, -0.7107), (0.7434, 0.6668, 0.0516)4.813, -4.166, -6.541
2given(0.4413, -0.5566, 0.7039), (0.4966, -0.5018, -0.7082), (0.7474, 0.6621, 0.055)5.079, -4.209, -6.705

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein PROTEIN (BACTERIORHODOPSIN) / BR


Mass: 26740.330 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SCHIFF BASE BETWEEN LYS 216 AND RET 999 / Source: (natural) Halobacterium salinarum (Halophile) / Cellular location: MEMBRANE / Strain: R1 / References: UniProt: P02945

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 584.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalp[3S]b1-6DManpa1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1122h-1a_1-5][a2112h-1b_1-5_3*OSO/3=O/3=O]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(2+1)][a-D-Manp]{[(6+1)][b-D-Galp3SO3]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 17 molecules

#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-ARC / 3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL


Mass: 298.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.2 / Details: SEE REFERENCE 2, pH 5.2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / PH range low: 5.6 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-11.5 mg/mlprotein1drop
20.25 %(w/v)beta-octylglucopyranoside1drop
32 %(w/v)benzamidine1drop
4250 mMsodium phosphate1drop
51.5 Msodium phosphate1drop
61.8-2.3 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 18504 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.2
Reflection shellResolution: 2.9→3.03 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.7 / % possible all: 43.6
Reflection
*PLUS
Num. measured all: 48145
Reflection shell
*PLUS
% possible obs: 43.6 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BRD

2brd


Resolution: 2.9→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 530 3 %SPHERICAL SHELLS
Rwork0.256 ---
obs0.256 18113 83.2 %-
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.6 Å20 Å224.1 Å2
2--36.4 Å20 Å2
3----101.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 376 0 5672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.252
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.191
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.2841.302
X-RAY DIFFRACTIONx_mcangle_it2.2022.243
X-RAY DIFFRACTIONx_scbond_it1.6221.666
X-RAY DIFFRACTIONx_scangle_it2.3422.437
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Weight Biso
22RESTRAINTSX-RAY DIFFRACTION6.0076.291
33X-RAY DIFFRACTION6.0076.291
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 34 3 %
Rwork0.214 1027 -
obs--43.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARRETIN.PROTOPRETIN.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.43
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.191
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.297 / % reflection Rfree: 3 % / Rfactor Rwork: 0.214

+
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://pdbjlvh1.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