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Yorodumi- PDB-1jbo: The 1.45A Three-Dimensional Structure of c-Phycocyanin from the T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jbo | ||||||
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Title | The 1.45A Three-Dimensional Structure of c-Phycocyanin from the Thermophylic Cyanobacterium Synechococcus elongatus | ||||||
Components |
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Keywords | PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Nield, J. / Rizkallah, P.J. / Barber, J. / Chayen, N.E. | ||||||
Citation | Journal: J.STRUCT.BIOL. / Year: 2003 Title: The 1.45A three-dimensional structure of C-phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus Authors: Nield, J. / Rizkallah, P.J. / Barber, J. / Chayen, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jbo.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jbo.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jbo ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jbo | HTTPS FTP |
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-Related structure data
Related structure data | 1cpcS 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the contents of the asymmetric unit by applying the operations: -y,x-y+1,z ; -x+y-1,-x,z ; y-1,x+1,-z ; x-y,-y+1,-z ; -x-1,-x+y,-z |
-Components
#1: Protein | Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P50032 | ||
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#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P50033 | ||
#3: Chemical | #4: 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: 2.88 Å3/Da / Density % sol: 57.36 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: Ammonium Sulphate, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
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: SRS / Beamline: PX14.1 / Wavelength: 1.244 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2000 |
Radiation | Monochromator: Sagitally focused Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→56.7 Å / Num. obs: 71757 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 16.34 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10410 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 95 Å / Num. measured all: 485268 |
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 10410 / Num. measured obs: 39957 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1CPC Resolution: 1.45→56.7 Å / Isotropic thermal model: Mixed isotropic and anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: REFMAC5 4.1 / Details: Weighted diagonal matrix
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Displacement parameters | Biso mean: 16.47 Å2
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Refine analyze | Luzzati coordinate error free: 0.0602 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→56.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å
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Refinement | *PLUS Lowest resolution: 95 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.53 Å / % reflection Rfree: 241 % / Num. reflection Rwork: 4882 |