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- PDB-1qko: HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qko | ||||||
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Title | HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE | ||||||
![]() | BACTERIORHODOPSIN | ||||||
![]() | PHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / INTERMEDIATE STATE / PHOTOCYCLE / LIPIDIC CUBIC PHASES | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Edman, K. / Nollert, P. / Royant, A. / Belrhali, H. / Pebay-Peyroula, E. / Hajdu, J. / Neutze, R. / Landau, E.M. | ||||||
![]() | ![]() 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: ![]() 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 |
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Remark 650 | HELIX DETERMINATION METHOD: DSSP | ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.3 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 655.4 KB | Display | ![]() |
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Full document | ![]() | 660.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qkpC ![]() 1qhjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | 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) ![]() |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density 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 | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / 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: unknownDetails: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.1→2.2 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QHJ Resolution: 2.1→38 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THIS STRUCTURE WAS REFINED AGAINST EXTRAPOLATED STRUCTURE FACTORS AS DESCRIBED BELOW. THE STRUCTURE FACTORS FROM AN ILLUMINATED CRYSTAL REPRESENTING A MIXTURE OF THE GROUND STATE AND THE LOW ...Details: THIS STRUCTURE WAS REFINED AGAINST EXTRAPOLATED STRUCTURE FACTORS AS DESCRIBED BELOW. THE STRUCTURE FACTORS FROM AN ILLUMINATED CRYSTAL REPRESENTING A MIXTURE OF THE GROUND STATE AND THE LOW TEMPERATURE K STATE OF BACTERIORHODOPSIN WHERE COMBINED WITH THE STRUCTURE FACTORS OF GROUND STATE DATA (R1QHJSF) CONSIDERING 35% OF EXCITED STATE AND 65% OF GROUND STATE. 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. THESE 9 RESIDUES WERE REFINED AGAINST EXTRAPOLATED STRUCTURE F.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 112 Å2 / ksol: 0.513 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.3033 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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