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Yorodumi- PDB-4ukd: UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ukd | ||||||
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Title | UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE | ||||||
Components | URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER / TRANSITION STATE ANALOG COMPLEX | ||||||
Function / homology | Function and homology information pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / CDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / (d)CMP kinase activity / phosphotransferase activity, phosphate group as acceptor / UMP kinase activity ...pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / CDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / (d)CMP kinase activity / phosphotransferase activity, phosphate group as acceptor / UMP kinase activity / UDP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å | ||||||
Authors | Schlichting, I. / Reinstein, J. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Authors: Schlichting, I. / Reinstein, J. #1: Journal: Biochemistry / Year: 1996 Title: Crystal Structure of the Complex of Ump/Cmp Kinase from Dictyostelium Discoideum and the Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Uridyl) Pentaphosphate (Up5A) and Mg2+ at 2.2 A: ...Title: Crystal Structure of the Complex of Ump/Cmp Kinase from Dictyostelium Discoideum and the Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Uridyl) Pentaphosphate (Up5A) and Mg2+ at 2.2 A: Implications for Water-Mediated Specificity Authors: Scheffzek, K. / Kliche, W. / Wiesmuller, L. / Reinstein, J. #2: Journal: FEBS Lett. / Year: 1995 Title: Crystallization and Preliminary X-Ray Analysis of Ump/Cmp-Kinase from Dictyostelium Discoideum with the Specific Bisubstrate Inhibitor P1-(Adenosine 5')-P5-(Uridine 5')-Pentaphosphate (Up5A) Authors: Wiesmuller, L. / Scheffzek, K. / Kliche, W. / Goody, R.S. / Wittinghofer, A. / Reinstein, J. #3: Journal: J.Biol.Chem. / Year: 1990 Title: Cdna-Derived Sequence of Ump-Cmp Kinase from Dictyostelium Discoideum and Expression of the Enzyme in Escherichia Coli Authors: Wiesmuller, L. / Noegel, A.A. / Barzu, O. / Gerisch, G. / Schleicher, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ukd.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ukd.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ukd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ukd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ukd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ukd_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4ukd_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/4ukd ftp://data.pdbj.org/pub/pdb/validation_reports/uk/4ukd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21970.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX2-214 / Gene: KCY_DICDI / Plasmid: PIMS5-CDUK-1 / Gene (production host): KCY_DICDI / Production host: Escherichia coli (E. coli) / References: UniProt: P20425, UMP/CMP kinase |
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-Non-polymers , 5 types, 111 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-UDP / |
#5: Chemical | ChemComp-BF2 / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | BEF2 LINKS THE TWO NUCLEOTIDE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→39 Å / Num. obs: 18420 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.366 / % possible all: 81 |
Reflection | *PLUS Num. measured all: 136023 |
Reflection shell | *PLUS % possible obs: 81 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2→39 Å / σ(F): 0
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5 % |