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Open data
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Basic information
Entry | Database: PDB / ID: 2bef | ||||||
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Title | CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3 | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | PHOSPHOTRANSFERASE / NUCLEOSIDE DIPHOSPHATE KINASE / PHOSPHORYL TRANSFER / BERYLLIUM FLUORIDE | ||||||
Function / homology | ![]() dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, Y.W. / Cherfils, J. | ||||||
![]() | ![]() Title: AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Authors: Xu, Y.W. / Morera, S. / Janin, J. / Cherfils, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.1 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE DICTYOSTELIUM NDP KINASE HEXAMER IS RECONSTITUTED FROM THE TRIMER IN THE ASYMMETRIC UNIT FROM CRYSTALLOGRAPHIC SYMMETRIES. THE POSITION OF BE++ WAS MODELLED IN TETRAHEDRAL CONFORMATION FROM THE ELECTRON DENSITY OF THE 3 FLUORINE ATOMS. |
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Components
#1: Protein | Mass: 16816.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ADP, BEF3, MG++ / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 38 % / Description: 100% IDENTITY | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: HANGING DROP, SEEDING, 32% PEG550, 50MM TRIS PH 7.5, 20MM MGCL2, 25MM NAF, 1MM BECL2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 20554 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.053 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.6 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 51271 / Rmerge(I) obs: 0.053 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 18.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 20058 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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