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Yorodumi- PDB-2f93: K Intermediate Structure of Sensory Rhodopsin II/Transducer Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f93 | ||||||
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Title | K Intermediate Structure of Sensory Rhodopsin II/Transducer Complex in Combination with the Ground State Structure | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / MENBRANE PROTEIN COMPLEX / SIGNAL TRANSDUCTION / PHOTOCYCLE STATE | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / monoatomic ion channel activity / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Natronomonas pharaonis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Moukhametzianov, R.I. / Klare, J.P. / Efremov, R.G. / Baecken, C. / Goeppner, A. / Labahn, J. / Engelhard, M. / Bueldt, G. / Gordeliy, V.I. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Development of the signal in sensory rhodopsin and its transfer to the cognate transducer. Authors: Moukhametzianov, R. / Klare, J.P. / Efremov, R. / Baeken, C. / Goppner, A. / Labahn, J. / Engelhard, M. / Buldt, G. / Gordeliy, V.I. #1: Journal: Nature / Year: 2002 Title: Molecular basis of transmembrane signalling by sensory rhodopsin II - transducer complex Authors: Gordeliy, V.I. / Labahn, J. / Moukhametzianov, R.I. / Efremov, R. / Granzin, J. / Schlesinger, R. / Bueldt, G. / Savapol, T. / Schedig, A.J. / Klare, J.P. / Engelhard, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f93.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f93.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 2f93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f93 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f93 | HTTPS FTP |
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-Related structure data
Related structure data | 2f95C 1h2sS 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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Number of models | 2 | ||||||||
Details | Functional K state is thought to consist of one ground state complex of sensory rhoodpsin II/transducer and one K state complex which is to be generated by applying the two fold operator to the K state: 1-x, -y, z |
-Components
#1: Protein | Mass: 26534.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Plasmid: PET27BMOD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42196 |
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#2: Protein | Mass: 12548.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htr2, htrII / Plasmid: PET27BMOD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42259 |
#3: Sugar | ChemComp-BOG / |
#4: Chemical | ChemComp-RET / |
#5: 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: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 295 K / pH: 5.8 Details: 150 MM NACL, 25 MM NAKPI 5.1 0.8% B-OCTYLGLUCOSID , MONOVACCENIN (CUBIC PHASE) PRECIPITATED BY 1 M NA/KPI 5.8 , in cubic lipidic phase, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.06 Å / Num. all: 22023 / Num. obs: 21010 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.494 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1H2S Resolution: 2→34.06 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1775916.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: MODEL USED FOR REFINEMENT CONSISTS OF GROUND STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR A AT POSITION 17) AND K STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR B AT POSITION 17) ...Details: MODEL USED FOR REFINEMENT CONSISTS OF GROUND STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR A AT POSITION 17) AND K STATE COMPLEX (ALTERNATIVE CONFORMATION INDICATOR B AT POSITION 17) WITH CORRESPONDING OCCUPANCIES. GROUND STATE MODEL WAS FIRST REFINED AGAINST THE GROUND STATE DATA AND THEN THE K STATE MODEL WAS REFINED WITH GROUND STATE MODEL FIXED AGAINST THE ILLUMINATED CRYSTAL DATA
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.103 Å2 / ksol: 0.453145 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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