+Open data
-Basic information
Entry | Database: PDB / ID: 2j9r | ||||||
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Title | Thymidine kinase from B. anthracis in complex with dT. | ||||||
Components | THYMIDINE KINASE | ||||||
Keywords | TRANSFERASE / TK1 / DNK / LASSO / KINASE / ATP-BINDING / DEOXYRIBONUCLEOSIDE KINASE / DNA SYNTHESIS / PHOSPHATE ACCEPTOR / NUCLEOTIDE-BINDING | ||||||
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 ANTHRACIS (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 2j9r.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j9r.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j9r_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 2j9r_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 2j9r_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2j9r_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9r ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9r | HTTPS FTP |
-Related structure data
Related structure data | 2ja1C 1xmr 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: 23841.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: STERNE / Variant: 34F2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q81JX0, thymidine kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-THM / |
#4: Chemical | ChemComp-PO4 / |
#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: 3.1 Å3/Da / Density % sol: 60.6 % |
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Crystal grow | pH: 6 Details: 5% 1,2-PROPANEDIOL 0.1M NA/K PHOSPHATE PH 6 10% GLYCEROL |
-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: 2.7→25.87 Å / Num. obs: 8799 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDP ENTRY 1XMR 1xmr Resolution: 2.7→25.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.998 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.276 / 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: 42.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→25.87 Å
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Refine LS restraints |
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