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Yorodumi- PDB-2vea: The complete sensory module of the cyanobacterial phytochrome Cph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vea | ||||||
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Title | The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state. | ||||||
Components | PHYTOCHROME-LIKE PROTEIN CPH1 | ||||||
Keywords | TRANSFERASE / ARGININE FINGER / PHOSPHORYLATION / TANDEM GAF DOMAIN / KNOT / KINASE / RECEPTOR / PAS DOMAIN / CHROMOPHORE / SENSORY TRANSDUCTION / PHOTORECEPTOR PROTEIN / BILIN-LIKE CHROMOPHORE / PHYTOCHROME / PHOTORECEPTOR | ||||||
Function / homology | Function and homology information response to red or far red light / red or far-red light photoreceptor activity / red, far-red light phototransduction / protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay sensor kinase activity / protein autophosphorylation / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | SYNECHOCYSTIS SP. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å | ||||||
Authors | Essen, L.-O. / Mailliet, J. / Hughes, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: The Structure of a Complete Phytochrome Sensory Module in the Pr Ground State. Authors: Essen, L.-O. / Mailliet, J. / Hughes, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vea.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vea.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2vea ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2vea | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58765.488 Da / Num. of mol.: 1 / Fragment: SENSORY MODULE, RESIDUES 1-514 Source method: isolated from a genetically manipulated source Details: THIOETHER LINKAGE BETWEEN C259 AND C3(1) ATOM OF PHYCOCYANOBILIN CHROMOPHORE Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Plasmid: P926.5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): P45.2 / References: UniProt: Q55168 | ||
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#2: Chemical | ChemComp-CYC / | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | PHYCOCYANOSequence details | TRANSMITTE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 55.5 % Description: DUE TO STRONG ANISOTROPISM OF THE CRYSTALS, DIFFRACTION DATA WERE RESCALED USING THE DIFFRACTION ANISOTROPY SERVER. THE FOLLOWING ANISOTROPIC CORRECTION WAS APPLIED TO THE NATIVE ...Description: DUE TO STRONG ANISOTROPISM OF THE CRYSTALS, DIFFRACTION DATA WERE RESCALED USING THE DIFFRACTION ANISOTROPY SERVER. THE FOLLOWING ANISOTROPIC CORRECTION WAS APPLIED TO THE NATIVE DATASETS, VALUES GIVEN IN SQUARE- ANGSTROM, -35.88,-35.88,17.94. THE COMPLETENESS OF THE NATIVE DATASET AT 2.7 ANGSTROM RESOLUTION WAS 98.5 PERCENT |
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Crystal grow | pH: 6.7 Details: TETRAGONAL CRYSTALS OF THE CPH1 PR STATE WERE GROWN IN 96-WELL CRYSTALLIZATION PLATES USING DROPS COMPRISING 500 NL 10 MG/ML CPH1-DELTA2 IN 2.5 MM TRIS/HCL PH 7.8, 15 MM NACL PLUS 500 NL ...Details: TETRAGONAL CRYSTALS OF THE CPH1 PR STATE WERE GROWN IN 96-WELL CRYSTALLIZATION PLATES USING DROPS COMPRISING 500 NL 10 MG/ML CPH1-DELTA2 IN 2.5 MM TRIS/HCL PH 7.8, 15 MM NACL PLUS 500 NL RESERVOIR SOLUTION (2.1 M SODIUM ACETATE, PH 6.7). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2007 / Details: MIRRORS |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 26939 / % possible obs: 67.2 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 6.7 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.21→24.68 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.506 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.PHYTOCHROME CRYSTAL IS IN THE PR STATE. DISORDERED LOOP REGIONS (Q73-R80, G100-D101, R148-Q150, E463- G465) ARE NOT INCLUDED IN MODEL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→24.68 Å
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