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Yorodumi- PDB-1otd: STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1otd | ||||||
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Title | STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE | ||||||
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: 1.25 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 999 | SEQRES Author states the sequence from the PYP was cloned from the strain SL-1 of ...SEQRES Author states the sequence from the PYP was cloned from the strain SL-1 of Ectothiorhodospira halophila, and there was no appropriate sequence database reference available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1otd.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1otd.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 1otd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1otd ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1otd | HTTPS FTP |
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-Related structure data
Related structure data | 1ot6C 1ot9C 1otaC 1otbC 1oteC 1otiC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13886.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: PYP / Production host: Escherichia coli (E. coli) / Strain (production host): SL-1 / References: UniProt: P16113 #2: Chemical | ChemComp-HC4 / #3: Water | ChemComp-HOH / | |
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-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: 39.88 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 4000, MgCl2, Tris, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K |
-Data collection
Diffraction | Mean temperature: 110 K |
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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: Nov 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→100 Å / Num. all: 61494 / Num. obs: 61494 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 56.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PHY Resolution: 1.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: derived from 1.0A (110K) wild type ground state structure
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Refinement step | Cycle: LAST / Resolution: 1.25→20 Å
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Refine LS restraints |
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