+Open data
-Basic information
Entry | Database: PDB / ID: 2pyr | ||||||
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Title | PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K) | ||||||
Components | PHOTOACTIVE YELLOW PROTEIN | ||||||
Keywords | PHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Halorhodospira halophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Perman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. ...Perman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K. | ||||||
Citation | Journal: Science / Year: 1998 Title: Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle. Authors: Perman, B. / Srajer, V. / Ren, Z. / Teng, T. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K. #1: Journal: Biochemistry / Year: 1995 Title: 1.4 A Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore Authors: Borgstahl, G.E. / Williams, D.R. / Getzoff, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pyr.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pyr.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2pyr ftp://data.pdbj.org/pub/pdb/validation_reports/py/2pyr | 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: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIOESTER LINK BETWEEN SG CYS 69 AND C1 HC4 150 / Source: (gene. exp.) Halorhodospira halophila (bacteria) / Strain: BN9626 Description: 4-HYDROXY CINNAMIC ANHYDRIDE CHROMOPHORE RECONSTITUTION Gene: P16113 / Plasmid: M15-PHISP / Production host: Escherichia coli (E. coli) / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
#3: 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: 1.9 Å3/Da / Density % sol: 35.17 % / Description: INITIAL PHASES ARE FROM 2PHY | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.3 |
Detector | Type: THOMPSON / Detector: CCD AREA DETECTOR / Date: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 13027 / % possible obs: 83.4 % / Redundancy: 14 % / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 14 % / % possible all: 44.8 |
Reflection shell | *PLUS % possible obs: 44.8 % |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / % reflection Rfree: 10 % / Cross valid method: FREE-R Details: TERWILLIGER/BERENDZEN DIFFERENCE REFINEMENT G RESIDUE IS DARK STRUCTURE, PG R RESIDE IS 1 NANOSECOND STRUCTURE, [PR]. ONLY DIFFERENT CONFORMATIONS AFTER 1 NANOSECOND INCLUDED. | ||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.185 | ||||||||||||||
Solvent computation | *PLUS | ||||||||||||||
Displacement parameters | *PLUS |