+Open data
-Basic information
Entry | Database: PDB / ID: 1h68 | ||||||
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Title | sensory rhodopsin II | ||||||
Components | SENSORY RHODOPSIN II | ||||||
Keywords | RECEPTOR / ARCHAEAL RHODOPSIN / PHOTORECEPTOR / PHOTOTAXIS | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | NATRONOMONAS PHARAONIS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Royant, A. / Nollert, P. / Edman, K. / Neutze, R. / Landau, E.M. / Pebay-Peyroula, E. / Navarro, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: X-Ray Structure of Sensory Rhodopsin II at 2.1 A Resolution Authors: Royant, A. / Nollert, P. / Edman, K. / Neutze, R. / Landau, E.M. / Pebay-Peyroula, E. / Navarro, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h68.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h68.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1h68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h68 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h68 | HTTPS FTP |
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-Related structure data
Related structure data | 1qhjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25368.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NATRONOMONAS PHARAONIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42196 |
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#2: Chemical | ChemComp-RET / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % Description: SIDE CHAINS, LOOPS AND THE RETINAL WERE OMITTED IN THE STARTING MODEL FOR MOLECULAR REPLACEMENT | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Date: Oct 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.9 Å / Num. obs: 15956 / % possible obs: 96.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.8 / % possible all: 80.1 |
Reflection | *PLUS Num. measured all: 99617 |
Reflection shell | *PLUS % possible obs: 80.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QHJ Resolution: 2.1→39.9 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FALT MODEL / Bsol: 113.25 Å2 / ksol: 0.48 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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