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- PDB-1kg8: X-ray structure of an early-M intermediate of bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1kg8
TitleX-ray structure of an early-M intermediate of bacteriorhodopsin
Componentsbacteriorhodopsin
KeywordsPROTON TRANSPORT / bacteriorhodopsin / intermediate / m-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: 2 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 1.3Aug 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 1.4Oct 30, 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)27,5045
Polymers25,3021
Non-polymers2,2024
Water23413
1
A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,51115
Polymers75,9063
Non-polymers6,60512
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 area11040 Å2
ΔGint-89 kcal/mol
Surface area23660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.745, 60.745, 108.240
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.: 3 / Source method: obtained synthetically / Formula: C42H86O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: mono-olein cubic phase / pH: 5.6
Details: 3.0M Na/K Phosphate, pH 5.6, mono-olein cubic phase, temperature 293K
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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 1999
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 14618 / Num. obs: 14618 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2→2.1 Å / % possible all: 91
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 95 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C8S

1c8s


Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.217 1210 Thin resolution shells
Rwork0.168 --
obs0.168 14618 -
all-14618 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 57 13 1738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg0.022
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 13408 / Rfactor all: 0.237 / Rfactor obs: 0.222 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_angle_d0.022

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