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- PDB-1kme: CRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES -

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Basic information

Entry
Database: PDB / ID: 1kme
TitleCRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN
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
beta-D-glucopyranose / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFaham, S. / Bowie, J.U.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure.
Authors: Faham, S. / Bowie, J.U.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN The identification of the lipid fragment as SQU is simply a guess.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2948
Polymers50,6042
Non-polymers1,6916
Water2,198122
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3484
Polymers25,3021
Non-polymers1,0463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9474
Polymers25,3021
Non-polymers6453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.000, 108.900, 55.900
Angle α, β, γ (deg.)90.00, 113.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe two molecules in the asymmetric unit are related by this rotation matrix : ( 0.99998 0.00411 -0.00372 ) ( 0.00410 -0.99999 -0.00269 ) ( -0.00373 0.00268 -0.99999 ) and this translation ( -22.61935 103.36683 34.80453 )

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Components

#1: Protein Bacteriorhodopsin / / BR


Mass: 25301.916 Da / Num. of mol.: 2 / Fragment: Residues 14-244 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-SQU / 2,10,23-TRIMETHYL-TETRACOSANE / LIPID FRAGMENT


Mass: 380.734 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H56
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop, bicelle method / pH: 3.5
Details: sodium phosphate, DMPC, Chapso, pH 3.5, VAPOR DIFFUSION, HANGING DROP, Bicelle Method, temperature 310.0K
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.0 mg/mlbR1drop
28 %bicell1drop
32.5 %beta-octylglucoside1drop
43.2 Msodium phosphate1reservoirpH3.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2001
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31440 / Num. obs: 31440 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.2 / % possible all: 62.5
Reflection
*PLUS
Num. measured all: 99274
Reflection shell
*PLUS
% possible obs: 62.5 % / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3W

1c3w


Resolution: 2→41.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1159567.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1610 5.2 %RANDOM
Rwork0.263 ---
all0.263 31440 --
obs0.263 31121 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 114.27 Å2 / ksol: 0.444285 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-2.49 Å2
2--2.15 Å20 Å2
3----3.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 104 122 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.142.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 210 5.4 %
Rwork0.283 3701 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4RET.PARRET.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scangle_it2.142.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.308 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.283

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