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- PDB-1qkp: HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE B... -

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Basic information

Entry
Database: PDB / ID: 1qkp
TitleHIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
ComponentsBACTERIORHODOPSIN
KeywordsPHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / INTERMEDIATE STATE / PHOTOCYCLE / LIPIDIC CUBIC PHASES
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARIUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEdman, K. / Nollert, P. / Royant, A. / Belrhali, H. / Pebay-Peyroula, E. / Hajdu, J. / Neutze, R. / Landau, E.M.
Citation
Journal: Nature / Year: 1999
Title: High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle.
Authors: Edman, K. / Nollert, P. / Royant, A. / Belrhali, H. / Pebay-Peyroula, E. / Hajdu, J. / Neutze, R. / Landau, E.M.
#1: Journal: Structure / Year: 1999
Title: Protein, Lipid and Water Organization in Bacteriorhodopsin: A Molecular View of the Purple Membrane at 1.9 Angstrom Resolution
Authors: Belrhali, H. / Nollert, P. / Royant, A. / Menzel, C. / Rosenbusch, J.P. / Landau, E.M. / Pebay-Peyroula, E.
History
DepositionJul 30, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_last / _citation.title
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.0May 22, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: DSSP
Remark 700 SHEET DETERMINATION METHOD: DSSP

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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)27,0992
Polymers26,8141
Non-polymers2841
Water48627
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2976
Polymers80,4433
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.060, 61.060, 110.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsA XRAY OBSERVED TRIMERIC BIO- ASSEMBLY CAN BE BUILTBY SPACE GROUP SYMMETRY EXPANSION OF THECONTENTS OF THE ASYMMETRIC UNIT

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Components

#1: 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 SALINARIUM (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Strain: S9 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48 %
Description: THE CRYSTAL FORM WAS THE SAME AS FOR 1QHJ, THEREFORE 1QHJ WAS DIRECTLY USED FOR THE INITIAL PHASING
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE ...Details: PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED 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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.936
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.1→38 Å / Num. obs: 13653 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.055 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 67437 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
CCP4data scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QHJ

1qhj


Resolution: 2.1→38 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: THIS STRUCTURE WAS REFINED FROM AN ILLUMINATED CRYSTAL AND REPRESENTS A MIXTURE OF THE GROUND STATE AND THE LOW TEMPERATURE K STATE OF BACTERIORHODOPSIN. DURING THE DATA COLLECTION, THE ...Details: THIS STRUCTURE WAS REFINED FROM AN ILLUMINATED CRYSTAL AND REPRESENTS A MIXTURE OF THE GROUND STATE AND THE LOW TEMPERATURE K STATE OF BACTERIORHODOPSIN. DURING THE DATA COLLECTION, THE CRYSTAL WAS MAINTAINED AT 110 K AND CONTINUOUSLY ILLUMINATED WITH A DIODE LASER AT 532 NM. THREE DATA SETS FROM ILLUMINATED CRYSTALS WERE COLLECTED. FROM THE 3 EXPERIMENTAL DIFFERENCE MAPS , FEXC-FGROUND (DATA IN R1QHJSF), 9 RESIDUES SHOWED SIGNIFICANT CHANGES IN THE EXCITED STATE. A FIRST REFINEMENT ON THE REMAINING RESIDUES WAS PERFORMED, FIXING THE 9 RESIDUES. THEN THESE 9 RESIDUES WERE REFINED WITH ALTERNATE CONFORMATIONS FIXING THE REMAINING STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 642 5 %THE SAME TEST SET AS FOR THE REFINEMENT OF 1QHJ WAS USED
Rwork0.2222 ---
obs0.2222 13628 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 90 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.566 Å20.292 Å20 Å2
2--4.566 Å20 Å2
3----9.132 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.01 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 20 27 1798
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0091
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_deg1.1637
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2305
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7917
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0811.5
X-RAY DIFFRACTIONc_mcangle_it1.4222
X-RAY DIFFRACTIONc_scbond_it1.7692
X-RAY DIFFRACTIONc_scangle_it2.0232.5
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2739 59 5 %
Rwork0.2239 1307 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3RETFIN.PARRETFIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.1637
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.2305
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7917

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