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Yorodumi- PDB-1ot9: CRYOTRAPPED STATE IN WILD TYPE PHOTOACTIVE YELLOW PROTEIN, INDUCE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ot9 | ||||||
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Title | CRYOTRAPPED STATE IN WILD TYPE PHOTOACTIVE YELLOW PROTEIN, INDUCED WITH CONTINUOUS ILLUMINATION AT 110K | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | LUMINESCENT PROTEIN / PYP / cryotrapping | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Anderson, S. / Crosson, S. / Moffat, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Short hydrogen bonds in photoactive yellow protein. Authors: Anderson, S. / Crosson, S. / Moffat, K. | ||||||
History |
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Remark 300 | BIOMOLECULE Model 1 is associated with the photoactivated state and Model 2 is associated with the ...BIOMOLECULE Model 1 is associated with the photoactivated state and Model 2 is associated with the ground state of the protein. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ot9.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ot9.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ot9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1ot9 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1ot9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ot6C 1otaC 1otbC 1otdC 1oteC 1otiC 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 |
-Components
#1: Protein | Mass: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: PYP / 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: 1.84 Å3/Da / Density % sol: 33.33 % Description: Author collected the first dataset in the dark, then a second dataset was collected on the same crystal after inducing a photostationary state with continuous illumination. The structure ...Description: Author collected the first dataset in the dark, then a second dataset was collected on the same crystal after inducing a photostationary state with continuous illumination. The structure was refined by the application of difference refinement to both datasets. |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 110K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2001 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1→100 Å / Num. all: 54493 / Num. obs: 54493 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.8 | |||||||||||||||
Reflection shell | Resolution: 1→1.04 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 7.2 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: derived from 1.0A 110K ground state structure
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Refinement step | Cycle: LAST / Resolution: 1→20 Å
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Refine LS restraints |
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