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- PDB-1qhj: X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES -

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Basic information

Entry
Database: PDB / ID: 1qhj
TitleX-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES
ComponentsPROTEIN (BACTERIORHODOPSIN)
KeywordsPHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDIC CUBIC PHASES / PURPLE MEMBRANE / ARCHEAL LIPIDS
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
Chem-PH1 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBelrhali, H. / Nollert, P. / Royant, A. / Menzel, C. / Rosenbusch, J.P. / Landau, E.M. / Pebay-Peyroula, E.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution.
Authors: Belrhali, H. / Nollert, P. / Royant, A. / Menzel, C. / Rosenbusch, J.P. / Landau, E.M. / Pebay-Peyroula, E.
History
DepositionMay 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN (BACTERIORHODOPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,83311
Polymers26,8141
Non-polymers6,01910
Water46826
1
A: PROTEIN (BACTERIORHODOPSIN)
hetero molecules

A: PROTEIN (BACTERIORHODOPSIN)
hetero molecules

A: PROTEIN (BACTERIORHODOPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,50033
Polymers80,4433
Non-polymers18,05730
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 area31470 Å2
ΔGint-226 kcal/mol
Surface area28860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.800, 60.800, 110.520
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 PROTEIN (BACTERIORHODOPSIN)


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RETINAL LINKED TO LYS 216 VIA A SCHIFF BASE / Source: (natural) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANE / Strain: S9 / 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-PH1 / 1,2-[DI-2,6,10,14-TETRAMETHYL-HEXADECAN-16-OXY]-PROPANE / PHYTANYL MOIETY


Mass: 637.158 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C43H88O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.39 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.6
Details: PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND RESOLVED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER ...Details: PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND RESOLVED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER AT PH 5.6, AT 20C AND IN THE DARK. THE MIXTURE WAS CENTRIFUGED AT 10000G FOR 150 MN PRIOR TO CRYSTALLISATION.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.3 Msodium potassium Pi11
23.5 mg/mlprotein11
30.05 %methylpentandiol11
41.2 %beta-octylglycopyranoside11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→38 Å / Num. obs: 17996 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.046 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.287 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 97807 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.287

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Processing

Software
NameVersionClassification
BASEDON PACKING CONSIDERATIONS NO SPECIAL SOFTWAREmodel building
CNS5refinement
XDSdata reduction
CCP4data scaling
BASEDON PACKING CONSIDERATIONS NO SPECIAL SOFTWAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AP9

1ap9


Resolution: 1.9→38 Å / Data cutoff high rms absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE DATA USED FOR THIS REFINEMENT WERE COLLECTED FROM A NON-TWINNED CRYSTAL. PROTEIN, RETINAL AND WATER ATOMS WERE REFINED. NINE PHYTANYL MOIETIES COULD THEN BE MODELED IN THE ELECTRON ...Details: THE DATA USED FOR THIS REFINEMENT WERE COLLECTED FROM A NON-TWINNED CRYSTAL. PROTEIN, RETINAL AND WATER ATOMS WERE REFINED. NINE PHYTANYL MOIETIES COULD THEN BE MODELED IN THE ELECTRON DENSITY MAPS. THE REFINEMENT STATISTICS GIVEN BELOW CORRESPOND TO THE REFINEMENT WITHOUT LIPID MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 869 5 %EXTENDED FROM THE PREVIOUS REFINEMENT 1AP9
Rwork0.224 ---
obs-17996 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20.588 Å20 Å2
2--3.17 Å20 Å2
3----6.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 425 26 2203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.183
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.72
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.718
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.262 113 5 %
Rwork0.272 2033 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMRETINAL.TOP
X-RAY DIFFRACTION3RETINAL.PAR
Software
*PLUS
Name: CNS / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.72
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.718
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % reflection Rfree: 5 %

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