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- PDB-1kgb: structure of ground-state bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1kgb
Titlestructure of ground-state bacteriorhodopsin
Componentsbacteriorhodopsin
KeywordsPROTON TRANSPORT / bacteriorhodopsin / ground-state
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 / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFacciotti, M.T. / Rouhani, S. / Burkard, F.T. / Betancourt, F.M. / Downing, K.H. / Rose, R.B. / McDermott, G. / Glaeser, R.M.
CitationJournal: Biophys.J. / Year: 2001
Title: Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle.
Authors: Facciotti, M.T. / Rouhani, S. / Burkard, F.T. / Betancourt, F.M. / Downing, K.H. / Rose, R.B. / McDermott, G. / Glaeser, R.M.
History
DepositionNov 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Refinement description / Category: exptl_crystal_grow / software / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,89515
Polymers25,3021
Non-polymers8,59314
Water48627
1
A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,68545
Polymers75,9063
Non-polymers25,77942
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 area26000 Å2
ΔGint-237 kcal/mol
Surface area27960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.987, 60.987, 109.131
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: 25301.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growMethod: mono-olein cubic phase / pH: 5.6
Details: 3.0M Na/K Phosphate, pH 5.6, mono-olein cubic phase, temperature 100K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 %OG11
23.0 Msodium potassium phosphate11pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 1999
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 26695 / Num. obs: 26695 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.8
Reflection shellResolution: 1.65→1.7 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.2 / % possible all: 96.8
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.358

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.65→20 Å / σ(F): 0 / Stereochemistry target values: NULL
RfactorNum. reflectionSelection details
Rfree0.188 1023 Thin resloution shells
Rwork0.13 --
obs0.13 26695 -
all-26695 -
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 303 27 2050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg0.034
X-RAY DIFFRACTIONo_bond_d0.017
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 25672 / σ(F): 0 / Rfactor all: 0.184 / Rfactor obs: 0.177 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_angle_deg

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