+Open data
-Basic information
Entry | Database: PDB / ID: 1uke | |||||||||
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Title | UMP/CMP KINASE FROM SLIME MOLD | |||||||||
Components | URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE | |||||||||
Keywords | NUCLEOTIDE MONOPHOSPHATE KINASE / NMP KINASE / NUCLEOTIDE SPECIFICITY / PHOSPHORYL TRANSFER / BISUBSTRATE INHIBITOR | |||||||||
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 / MIR (MIR) / Resolution: 2.2 Å | |||||||||
Authors | Scheffzek, K. / Kliche, W. / Wiesmueller, L. / Reinstein, J. | |||||||||
Citation | 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. #1: Journal: Protein Sci. / Year: 1995 Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer Authors: Abele, U. / Schulz, G.E. #2: Journal: Structure / Year: 1995 Title: Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases Authors: Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E. #3: Journal: J.Mol.Biol. / Year: 1995 Title: Substrate Specificity and Assembly of the Catalytic Center Derived from Two Structures of Ligated Uridylate Kinase Authors: Muller-Dieckmann, H.J. / Schulz, G.E. #4: 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. #5: 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 | 1uke.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uke.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uke_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 1uke_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 1uke_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1uke_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1uke ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1uke | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-UP5 / |
#4: 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: 3.56 Å3/Da / Density % sol: 65 % / Description: NUMBER OF MEASURED REFLECTIONS : 119529 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: SEE REFERENCE 4, pH 8. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.8 / Method: vapor diffusion, hanging drop / Details: Wiesmuller, L., (1995) FEBS Lett., 363, 22. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ELLIOTT / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Mar 9, 1993 / Details: NICKEL COATED FRANKS DOUBLE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 16642 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.2→2.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 119529 |
-Processing
Software |
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Refinement | Method to determine structure: MIR (MIR) Starting model: ADENYLATE KINASE (PORCINE), PDB ENTRY 1ADK3 Resolution: 2.2→8 Å / σ(F): 0 Details: SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT ENTIRELY WELL DEFINED IN THE DENSITY AND WERE MODELLED BY STEREOCHEMISTRY: LYS 2, GLU 3, LYS 5, LYS 50, GLU 53, LYS 60, LYS 72, GLN 82, LYS 106, ...Details: SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT ENTIRELY WELL DEFINED IN THE DENSITY AND WERE MODELLED BY STEREOCHEMISTRY: LYS 2, GLU 3, LYS 5, LYS 50, GLU 53, LYS 60, LYS 72, GLN 82, LYS 106, PHE 108, SER 135, ARG 137, LYS 146. IN THE CASE OF ARG 137 DENSITY FOR MAIN CHAIN ATOMS IS DISCONNECTIVE.
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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