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Yorodumi- PDB-1to0: X-ray structure of Northeast Structural Genomics target protein s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1to0 | ||||||
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Title | X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis | ||||||
Components | Hypothetical UPF0247 protein yyda | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Edstrom, W. / Vorobiev, S.M. / Shastry, R. / Ma, L.-C. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis Authors: Kuzin, A.P. / Edstrom, W. / Vorobiev, S.M. / Shastry, R. / Ma, L.-C. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1to0.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1to0.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 1to0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/1to0 ftp://data.pdbj.org/pub/pdb/validation_reports/to/1to0 | HTTPS FTP |
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-Related structure data
Related structure data | 1vh0S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19455.645 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YYDA, BSU40230 / Plasmid: pet21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45601 #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: 2.4 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18-20 % PEG 3350, 0.2 M KCl, 50 mM TrisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 113561 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.89 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.516 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VH0 Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 364813.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.3779 Å2 / ksol: 0.271662 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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