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Yorodumi- PDB-1wj9: Crystal structure of a CRISPR-associated protein from thermus the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wj9 | ||||||
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Title | Crystal structure of a CRISPR-associated protein from thermus thermophilus | ||||||
Components | CRISPR-associated protein | ||||||
Keywords | Structural genomics / unknown function / ALPHA AND BETA PROTEIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Ebihara, A. / Yao, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain Authors: Ebihara, A. / Yao, M. / Masui, R. / Tanaka, I. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wj9.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wj9.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wj9 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wj9 | 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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-Components
#1: Protein | Mass: 23763.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53WG9 |
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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: 3.1 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 20% PEGMME2000, 0.1M bicine, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 22655 / % possible obs: 98.1 % / Redundancy: 6 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 35.6 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2254 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→38.34 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1518252.71 / 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: 26.1594 Å2 / ksol: 0.334945 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→38.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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