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Yorodumi- PDB-2zop: X-ray crystal structure of a CRISPR-associated Cmr5 family protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zop | ||||||
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Title | X-ray crystal structure of a CRISPR-associated Cmr5 family protein from Thermus thermophilus HB8 | ||||||
Components | Putative uncharacterized protein TTHB164 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / All alpha proteins / Plasmid / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Sakamoto, K. / Agari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2009 Title: X-ray crystal structure of a CRISPR-associated RAMP superfamily protein, Cmr5, from Thermus thermophilus HB8 Authors: Sakamoto, K. / Agari, Y. / Agari, K. / Yokoyama, S. / Kuramitsu, S. / Shinkai, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zop.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zop.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zop_validation.pdf.gz | 480.4 KB | Display | wwPDB validaton report |
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Full document | 2zop_full_validation.pdf.gz | 492.1 KB | Display | |
Data in XML | 2zop_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 2zop_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/2zop ftp://data.pdbj.org/pub/pdb/validation_reports/zo/2zop | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13075.657 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHB164 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W05 #2: Chemical | ChemComp-SO4 / #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: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M sodium acetate, 1.7M ammonium sulfate, 0.03M DTT, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2007 Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium. |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 45600 / Num. obs: 45600 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 51.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 9.4 / Num. unique all: 4488 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→43.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4139235.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4646 Å2 / ksol: 0.379875 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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