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Yorodumi- PDB-1ktp: Crystal structure of c-phycocyanin of synechococcus vulcanus at 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ktp | ||||||
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Title | Crystal structure of c-phycocyanin of synechococcus vulcanus at 1.6 angstroms | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / CYANOBACTERIA / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / THERMOSTABILITY | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Adir, N. / Dobrovetsky, E. / Lerner, N. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2002 Title: Refined structure of c-phycocyanin from the cyanobacterium Synechococcus vulcanus at 1.6 A: insights into the role of solvent molecules in thermal stability and co-factor structure Authors: Adir, N. / Vainer, R. / Lerner, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ktp.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ktp.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ktp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1ktp ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1ktp | HTTPS FTP |
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-Related structure data
Related structure data | 1i7yS S: Starting model for refinement |
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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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3 |
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4 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 17470.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P50032 | ||
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#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria) References: UniProt: P50033 | ||
#3: Chemical | ChemComp-BLA / | ||
#4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 55.65 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% PEG4000, 50MM HEPES, 5MG/ML PROTEIN, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Details: Adir, N., (2001) J. Mol. Biol., 313, 71. | ||||||||||||||||||||
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: CHESS / Beamline: A1 / Wavelength: 0.928 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 47823 / Num. obs: 47798 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 87.4 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 51656 / % possible obs: 97.5 % / Redundancy: 5.6 % / Num. measured all: 419135 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I7Y Resolution: 1.6→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 35632 / % reflection Rfree: 7.7 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3195 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.28 / Num. reflection obs: 3977 / Rfactor obs: 0.302 |