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Yorodumi- PDB-2ywq: Crystal structure of Thermus thermophilus Protein Y N-terminal domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ywq | ||||||
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Title | Crystal structure of Thermus thermophilus Protein Y N-terminal domain | ||||||
Components | Ribosomal subunit interface protein | ||||||
Keywords | RIBOSOMAL PROTEIN / Sigma-54 modulation protein family / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of translational elongation / ribosomal small subunit binding / cytosolic small ribosomal subunit Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å | ||||||
Authors | Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Saito, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Thermus thermophilus Protein Y N-terminal domain Authors: Kawazoe, M. / Takemoto, C. / Kaminishi, T. / Tatsuguchi, A. / Saito, Y. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ywq.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ywq.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ywq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ywq_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
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Full document | 2ywq_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 2ywq_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2ywq_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/2ywq ftp://data.pdbj.org/pub/pdb/validation_reports/yw/2ywq | HTTPS FTP |
-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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12255.760 Da / Num. of mol.: 4 / Fragment: N-terminal domain, residues 1-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1294 / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SIS0 #2: 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: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 4M Sodium formate, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97909, 0.97928, 0.96405 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.64→44.28 Å / Num. obs: 14256 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 27.84 % / Biso Wilson estimate: 64 Å2 / Rsym value: 0.114 / Net I/σ(I): 28.52 | ||||||||||||
Reflection shell | Resolution: 2.64→2.73 Å / Redundancy: 28.2 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 1371 / Rsym value: 0.61 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.64→44.13 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1998698.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.7124 Å2 / ksol: 0.37534 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.64→44.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.81 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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