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Yorodumi- PDB-2a30: Crystal structure of human deoxycytidine kinase in complex with d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a30 | ||||||
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Title | Crystal structure of human deoxycytidine kinase in complex with deoxycytidine | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / Nucleoside kinase | ||||||
Function / homology | Function and homology information deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | ||||||
Authors | Godsey, M.H. / Ort, S. / Sabini, E. / Konrad, M. / Lavie, A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization. Authors: Godsey, M.H. / Ort, S. / Sabini, E. / Konrad, M. / Lavie, A. | ||||||
History |
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Remark 600 | HETEROGEN DCZ 302 are assoicated with protein chain A DCZ 402 are assoicated with protein chain B ...HETEROGEN DCZ 302 are assoicated with protein chain A DCZ 402 are assoicated with protein chain B DCZ 502 are assoicated with protein chain C DCZ 602 are assoicated with protein chain D |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a30.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a30.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 2a30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/2a30 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/2a30 | HTTPS FTP |
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-Related structure data
Related structure data | 2a2zC 1p60S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Biological assembly is a dimer. There are two dimers per ASU. |
-Components
#1: Protein | Mass: 29139.004 Da / Num. of mol.: 4 / Mutation: residues 65-79 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P27707, deoxycytidine kinase #2: Chemical | #3: Chemical | ChemComp-DCZ / #4: 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: 48.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 1000, MPD, Calcium Chloride, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97626 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 8, 2004 / Details: MIRROR |
Radiation | Monochromator: Sagittaly focused Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 22365 / Num. obs: 20040 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.141 / Rsym value: 0.118 / Net I/σ(I): 8.77 |
Reflection shell | Resolution: 3→3.1 Å / % possible obs: 53.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.36 / Num. measured obs: 3602 / Num. unique all: 1124 / Num. unique obs: 1124 / Rsym value: 0.542 / % possible all: 81.2 |
-Phasing
Phasing MR | Rfactor: 52.1 / Cor.coef. Fo:Fc: 37.2 / Cor.coef. Io to Ic: 42.9
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1P60 Resolution: 3.02→19.9 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 34.1324 Å2 / ksol: 0.230619 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.84 Å2 / Biso mean: 69.89 Å2 / Biso min: 22.85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.02→19.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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