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- PDB-1qf9: PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qf9 | ||||||
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Title | PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL TRANSFER TRANSITION STATE ANALOG IN UMP/CMP KINASE | ||||||
![]() | PROTEIN (URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE) | ||||||
![]() | KINASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER / TRANSITION STATE ANALOG COMPLEX / TRANSFERASE | ||||||
Function / homology | ![]() pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / phosphotransferase activity, phosphate group as acceptor / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity ...pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / phosphotransferase activity, phosphate group as acceptor / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleoside diphosphate kinase activity / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlichting, I. / Reinstein, J. | ||||||
![]() | ![]() Title: pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog. Authors: Schlichting, I. / Reinstein, J. #1: ![]() Title: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Authors: Schlichting, I. / Reinstein, J. #2: ![]() 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. #3: 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. #4: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
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PDB format | ![]() | 42.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ukdC ![]() 3ukdS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 185 molecules ![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/C5P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/C5P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ALF / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: Chemical | ChemComp-C5P / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | ALF4 IS STABILIZED IN SOLUTION BY THE LOW PH USED FOR CRYSTALLIZATION ALF4 IS A SQUARE PLANAR ...ALF4 IS STABILIZED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 100 MM SODIUM ACETATE PH 4.5, 50 MM MGCL2, 40 MM DTE, 28% PEG 4000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 40853 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 23.19 Å2 / Rsym value: 0.082 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3 / Rsym value: 0.36 / % possible all: 95.1 |
Reflection | *PLUS Num. measured all: 255114 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 95.1 % / Rmerge(I) obs: 0.36 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UKD Resolution: 1.7→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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