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Yorodumi- PDB-1tev: Crystal structure of the human UMP/CMP kinase in open conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tev | ||||||
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Title | Crystal structure of the human UMP/CMP kinase in open conformation | ||||||
Components | UMP-CMP kinase | ||||||
Keywords | TRANSFERASE / Kinase / Ploop / NMP binding region / LID region / Conformational Changes | ||||||
Function / homology | Function and homology information UMP/CMP kinase / CDP biosynthetic process / nucleoside monophosphate kinase activity / cytidylate kinase activity / CMP kinase activity / dCMP kinase activity / uridine kinase activity / UMP kinase activity / pyrimidine ribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion ...UMP/CMP kinase / CDP biosynthetic process / nucleoside monophosphate kinase activity / cytidylate kinase activity / CMP kinase activity / dCMP kinase activity / uridine kinase activity / UMP kinase activity / pyrimidine ribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / UDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Segura-Pena, D. / Sekulic, N. / Ort, S. / Konrad, M. / Lavie, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Substrate-induced Conformational Changes in Human UMP/CMP Kinase. Authors: Sekulic, N. / Ort, S. / Konrad, M. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tev.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tev.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1tev ftp://data.pdbj.org/pub/pdb/validation_reports/te/1tev | HTTPS FTP |
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-Related structure data
Related structure data | 1ukeS 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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Unit cell |
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-Components
#1: Protein | Mass: 22253.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UCK / Plasmid: pGEX-RB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30085, UMP/CMP kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Magnesium Sulfate, Sodium Acetate, pH 4.6, 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: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 15467 / Num. obs: 15467 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 27.73075 Å2 / Rsym value: 0.116 / Net I/σ(I): 15.27 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 10.8 % / Num. unique all: 1737 / Rsym value: 0.393 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UKE Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.547 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.223 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.674 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.153 Å / Total num. of bins used: 20 /
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