+Open data
-Basic information
Entry | Database: PDB / ID: 1gue | ||||||
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Title | SENSORY RHODOPSIN II | ||||||
Components | SENSORY RHODOPSIN II | ||||||
Keywords | PHOTORECEPTOR / ARCHAEAL RHODOPSIN / 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: 2.27 Å | ||||||
Authors | Edman, K. / Royant, A. / Nollert, P. / Maxwell, C.A. / Pebay-Peyroula, E. / Navarro, J. / Neutze, R. / Landau, E.M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Early Structural Rearrangements in the Photocycle of an Integral Membrane Sensory Receptor Authors: Edman, K. / Royant, A. / Nollert, P. / Maxwell, C.A. / Pebay-Peyroula, E. / Navarro, J. / Neutze, R. / Landau, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gue.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gue.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gue ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gue | HTTPS FTP |
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-Related structure data
Related structure data | 1gu8C 1h68S S: Starting model for refinement C: citing same article (ref.) |
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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 Details: K-STATE, REFINED WITH EXTRAPOLATED DATA / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: Royant, A., (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 10131. | ||||||||||||||||||||||||||||||
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: ID14-3 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→35.6 Å / Num. obs: 13086 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.27→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.9 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H68 Resolution: 2.27→35.6 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 89.5 Å2 / ksol: 0.47 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.44 / Rfactor obs: 0.44 |