+Open data
-Basic information
Entry | Database: PDB / ID: 1odv | ||||||
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Title | Photoactive yellow protein 1-25 deletion mutant | ||||||
Components | PHOTOACTIVE YELLOW PROTEIN | ||||||
Keywords | SIGNALLING / PHOTOACTIVITY / P-COUMARIC ACID | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ECTOTHIORHODOSPIRA HALOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Vreede, J. / Van Der horst, M.A. / Hellingwerf, K.J. / Crielaard, W. / Van Aalten, D.M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Pas Domains.Common Structure and Common Flexibility Authors: Vreede, J. / Van Der Horst, M.A. / Hellingwerf, K.J. / Crielaard, W. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1odv.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1odv.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 1odv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/1odv ftp://data.pdbj.org/pub/pdb/validation_reports/od/1odv | HTTPS FTP |
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-Related structure data
Related structure data | 2phyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11181.659 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-125 Source method: isolated from a genetically manipulated source Details: P-COUMARIC ACID Source: (gene. exp.) ECTOTHIORHODOSPIRA HALOPHILA (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16113 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | PHOTOACTIVE BLUE-LIGHT PROTEIN THAT PROBABLY FUNCTIONS AS A PHOTORECEPTOR FOR A NEGATIVE PHOTOTAXIS ...PHOTOACTIV | |
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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: 2.07 Å3/Da / Density % sol: 40.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER ...Details: CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER LIQUOR. CRYSTALS APPEARED AFTER 2-3 DAYS A LARGEST DIMENSION OF 0.4 MM. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→17 Å / Num. obs: 299780 / % possible obs: 94.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.3 / % possible all: 89.2 |
Reflection | *PLUS Num. obs: 75208 / Num. measured all: 299780 |
Reflection shell | *PLUS % possible obs: 89.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PHY Resolution: 1.14→17 Å / Num. parameters: 17869 / Num. restraintsaints: 21180 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 1459 / Occupancy sum non hydrogen: 1919 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→17 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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