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- PDB-3idz: Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3idz | |||||||||
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Title | Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophilus HB8 | |||||||||
![]() | Ribonuclease TTHA0252 | |||||||||
![]() | HYDROLASE / metallo beta lactamase fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Endonuclease / Metal-binding / Nuclease / RNA-binding / rRNA processing | |||||||||
Function / homology | ![]() snRNA processing / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
![]() | ![]() Title: Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophilus HB8 Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.6 KB | Display | ![]() |
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PDB format | ![]() | 281.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.9 KB | Display | ![]() |
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Full document | ![]() | 592.8 KB | Display | |
Data in XML | ![]() | 69.7 KB | Display | |
Data in CIF | ![]() | 93.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dkfS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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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: 47159.125 Da / Num. of mol.: 4 / Mutation: S378Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5SLP1, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % / Mosaicity: 0.455 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50mM sodium citrate, 0.2M ammonium sulfate, 0.6M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.28244 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 81525 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.037 / Net I/σ(I): 16.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DKF Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 48.47 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.11 Å2 / Biso mean: 66.009 Å2 / Biso min: 18.62 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011
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Xplor file |
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