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- PDB-1q5j: Crystal structure of bacteriorhodopsin mutant P91A crystallized f... -

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Basic information

Entry
Database: PDB / ID: 1q5j
TitleCrystal structure of bacteriorhodopsin mutant P91A crystallized from bicelles
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / alpha helix
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYohannan, S. / Faham, S. / Yang, D. / Whitelegge, J.P. / Bowie, J.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors.
Authors: Yohannan, S. / Faham, S. / Yang, D. / Whitelegge, J.P. / Bowie, J.U.
History
DepositionAug 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3764
Polymers53,8072
Non-polymers5692
Water1,26170
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1882
Polymers26,9031
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1882
Polymers26,9031
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.527, 108.300, 55.818
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacteriorhodopsin / BR


Mass: 26903.463 Da / Num. of mol.: 2 / Mutation: P91A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Strain: L33 / Gene: BOP OR VNG1467G / Plasmid: pMPK85 / Production host: Escherichia coli (E. coli) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: DMPC, CHAPSO, sodium phosphate, hexanediol, pH 3.7, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 M1reservoirpH3.7NaH2PO4
20.09 Mhexanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→500 Å / Num. obs: 26254 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.18 Å / % possible all: 90.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PY6

1py6


Resolution: 2.1→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal twinning was observed. Twinning operation = -h, -k, h+l. Twinning fraction = 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1326 4.7 %SHELLS
Rwork0.216 ---
all0.218 28327 --
obs0.218 24928 88 %-
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 40 70 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.1131.5
X-RAY DIFFRACTIONc_scbond_it1.5852
X-RAY DIFFRACTIONc_mcangle_it1.7982
X-RAY DIFFRACTIONc_scangle_it2.2872.5
LS refinement shellHighest resolution: 2.1 Å / Num. reflection Rfree: 1326 / Num. reflection obs: 24928
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ret.param
Refinement
*PLUS
Rfactor Rfree: 0.267 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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