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Yorodumi- PDB-2ja1: Thymidine kinase from B. cereus with TTP bound as phosphate donor. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ja1 | ||||||
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Title | Thymidine kinase from B. cereus with TTP bound as phosphate donor. | ||||||
Components | THYMIDINE KINASE | ||||||
Keywords | TRANSFERASE / TK1 / DNK / LASSO / KINASE / PHOSPHATE DONOR / DEOXYRIBONUCLEOSIDE KINASE | ||||||
Function / homology | Function and homology information thymidine kinase / thymidine kinase activity / DNA biosynthetic process / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kosinska, U. / Carnrot, C. / Sandrini, M.P.B. / Clausen, A.R. / Wang, L. / Piskur, J. / Eriksson, S. / Eklund, H. | ||||||
Citation | Journal: FEBS J. / Year: 2007 Title: Structural Studies of Thymidine Kinases from Bacillus Anthracis and Bacillus Cereus Provide Insights Into Quaternary Structure and Conformational Changes Upon Substrate Binding Authors: Kosinska, U. / Carnrot, C. / Sandrini, M.P.B. / Clausen, A.R. / Wang, L. / Piskur, J. / Eriksson, S. / Eklund, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ja1.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ja1.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 2ja1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ja1_validation.pdf.gz | 806.3 KB | Display | wwPDB validaton report |
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Full document | 2ja1_full_validation.pdf.gz | 809.2 KB | Display | |
Data in XML | 2ja1_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2ja1_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2ja1 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2ja1 | HTTPS FTP |
-Related structure data
Related structure data | 2j9rSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21866.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: DVI / Variant: 98-7869 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KY895 References: UniProt: Q0H9H6, UniProt: Q0H0H6*PLUS, thymidine kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-TTP / |
#4: Chemical | ChemComp-MPD / ( |
#5: 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: 5.3 Å3/Da / Density % sol: 76.6 % |
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Crystal grow | pH: 7 / Details: 60% MPD 0.1M HEPES PH7, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.6 Å / Num. obs: 12035 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rrim(I) all: 0.1 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 14 % / Mean I/σ(I) obs: 4.2 / Rrim(I) all: 0.534 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J9R Resolution: 2.8→37.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 17.574 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→37.63 Å
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Refine LS restraints |
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