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Yorodumi- PDB-1v2z: Crystal structure of the C-terminal domain of Thermosynechococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v2z | ||||||
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Title | Crystal structure of the C-terminal domain of Thermosynechococcus elongatus BP-1 KaiA | ||||||
Components | circadian clock protein KaiA homolog | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / ALL ALPHA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Uzumaki, T. / Fujita, M. / Nakatsu, T. / Hayashi, F. / Shibata, H. / Itoh, N. / Kato, H. / Ishiura, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: NAT.STRUCT.MOL.BIOL. / Year: 2004 Title: Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein Authors: Uzumaki, T. / Fujita, M. / Nakatsu, T. / Hayashi, F. / Shibata, H. / Itoh, N. / Kato, H. / Ishiura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v2z.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v2z.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 1v2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/1v2z ftp://data.pdbj.org/pub/pdb/validation_reports/v2/1v2z | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. The second part of the biological assembly is generated by the two fold axis: y, x, -z+1 |
-Components
#1: Protein | Mass: 13186.209 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8RR35, UniProt: Q79V62*PLUS |
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#2: 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: 2.02 Å3/Da / Density % sol: 38.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: NaCl, Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 / Wavelength: 1.0, 0.96, 0.9792, 0.97957 | |||||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 28, 2003 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→27.5 Å / Num. all: 10611 / Num. obs: 10611 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.2 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.055 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.641 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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