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- PDB-1brr: X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX -

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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


phototransduction / photoreceptor activity / protein-chromophore linkage / ion channel activity / integral component of membrane / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / 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 / RETINAL / N-OCTANE / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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
γ
α
β
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

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Components

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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: MEMBRANEBiological membrane / Strain: R1 / References: UniProt: P02945

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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 / 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

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Non-polymers , 4 types, 17 molecules

#3: Chemical ChemComp-RET / RETINAL / 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 / Glycerol


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


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

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Experimental details

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Experiment

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

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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

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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 %

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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
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 2)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

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