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Yorodumi- PDB-2uz3: Crystal Structure of Thymidine Kinase with dTTP from U. urealyticum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uz3 | |||||||||
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Title | Crystal Structure of Thymidine Kinase with dTTP from U. urealyticum | |||||||||
Components | THYMIDINE KINASE | |||||||||
Keywords | TRANSFERASE / DEOXYRIBONUCLEOSIDE KINASE / ZINC-BINDING DOMAIN / FEED-BACK INHIBITOR / TK1 / DTTP / UU-TK / KINASE / ATP-BINDING / LASSO-DOMAIN / DNA SYNTHESIS / NUCLEOTIDE-BINDING | |||||||||
Function / homology | Function and homology information thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | UREAPLASMA UREALYTICUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Welin, M. / Kosinska, U. / Mikkelsen, N.E. / Carnrot, C. / Zhu, C. / Wang, L. / Eriksson, S. / Munch-Petersen, B. / Eklund, H. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structures of Thymidine Kinase 1 of Human and Mycoplasmic Origin Authors: Welin, M. / Kosinska, U. / Mikkelsen, N.E. / Carnrot, C. / Zhu, C. / Wang, L. / Eriksson, S. / Munch-Petersen, B. / Eklund, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uz3.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uz3.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uz3 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uz3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 27611.600 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) UREAPLASMA UREALYTICUM (bacteria) / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9PPP5, thymidine kinase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-TTP / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 16 TO PHE ENGINEERED RESIDUE IN CHAIN B, LEU 16 TO PHE ...ENGINEERED | Sequence details | THE TWENTY FIRTS RESIDUES (-19 - 0) CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000, LITHIUM CHLORIDE, DTT, REMARK 280 MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287.0 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 5, 2003 |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→60 Å / Num. obs: 33042 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 0.14 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.27 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.5→69.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.9 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.664 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→69.01 Å
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Refine LS restraints |
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