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- PDB-1brx: BACTERIORHODOPSIN/LIPID COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1brx
TitleBACTERIORHODOPSIN/LIPID COMPLEX
ComponentsBACTERIORHODOPSIN
KeywordsPROTON 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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLuecke, H. / Richter, H.T. / Lanyi, J.
CitationJournal: Science / Year: 1998
Title: Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution.
Authors: Luecke, H. / Richter, H.T. / Lanyi, J.K.
History
DepositionMay 28, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence / Refinement description
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0822
Polymers26,7971
Non-polymers2841
Water543
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2456
Polymers80,3923
Non-polymers8533
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 area6470 Å2
ΔGint-56 kcal/mol
Surface area24830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.850, 60.850, 108.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein BACTERIORHODOPSIN /


Mass: 26797.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKAGE BETWEEN LYS 126 (NZ) AND RET 301 (C15)
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Organ: PLASMA / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 43.08 % / Description: FLASH-COOLED IN LN2 STREAM
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein11
20.05 %methylpentanediol11
31.2 %beta-octylglycopyranoside11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 9769 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Rsym value: 0.113 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.443 / % possible all: 75.9
Reflection
*PLUS
Num. measured all: 250474 / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 75.9 % / Rmerge(I) obs: 0.443

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AT9 AND 2BRD

1at9

2brd


Resolution: 2.3→12 Å / Num. parameters: 6544 / Num. restraintsaints: 6912 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: USED TWIN OPTION, REFINED TWIN RATIO: 0.54/0.46.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 494 5 %THIN SHELLS
obs0.223 -96.5 %-
all-9696 --
Solvent computationSolvent model: SWAT
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 20 3 1635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d1.653
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
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): 4 / Rfactor all: 0.223 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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