+Open data
-Basic information
Entry | Database: PDB / ID: 1oti | ||||||
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Title | E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 295K | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / PYP | ||||||
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: 1.4 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oti.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oti.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1oti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oti_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 1oti_full_validation.pdf.gz | 431.4 KB | Display | |
Data in XML | 1oti_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1oti_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1oti ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1oti | HTTPS FTP |
-Related structure data
Related structure data | 1ot6C 1ot9C 1otaC 1otbC 1otdC 1oteC 2phyS 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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-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: 2.05 Å3/Da / Density % sol: 39.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. all: 21402 / Num. obs: 21402 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 23.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PHY Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: derived from 0.95A 110K E46Q mutant ground state structure
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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