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Yorodumi- PDB-1ot6: CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ot6 | ||||||
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Title | CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATION AT 110K | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING 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: 0.95 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 | 1ot6.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ot6.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ot6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1ot6 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1ot6 | HTTPS FTP |
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-Related structure data
Related structure data | 1ot9C 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: 13887.591 Da / Num. of mol.: 1 / Mutation: E46Q 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: 33.28 % 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: 0.95→100 Å / Num. all: 63595 / Num. obs: 63595 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5 | |||||||||||||||
Reflection shell | Resolution: 0.95→0.98 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 26.5 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 0.95→20 Å
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Refine LS restraints |
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