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Yorodumi- PDB-2yv4: Crystal Structure of C-terminal Sua5 Domain from Pyrococcus horik... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yv4 | ||||||
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Title | Crystal Structure of C-terminal Sua5 Domain from Pyrococcus horikoshii Hypothetical Sua5 Protein PH0435 | ||||||
Components | Hypothetical protein PH0435Hypothesis | ||||||
Keywords | RNA BINDING PROTEIN / Alpha and beta proteins (a+b) / Sua5 Domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / double-stranded RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Agari, Y. / Shinkai, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C-terminal Sua5 Domain from Pyrococcus horikoshii Hypothetical Sua5 Protein PH0435 Authors: Agari, Y. / Shinkai, A. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yv4.cif.gz | 29.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv4.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv4 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv4 | 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: 11582.152 Da / Num. of mol.: 1 / Fragment: Residues 236-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O73972 |
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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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 30% w/v PEG 8000, 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: 0.97886, 0.90, 0.97929 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 21, 2006 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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→40 Å / Num. all: 6812 / Num. obs: 6812 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 47.8 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 13.6 / Num. unique all: 658 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→31.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1128339.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.853 Å2 / ksol: 0.355844 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→31.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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