+Open data
-Basic information
Entry | Database: PDB / ID: 2bef | ||||||
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Title | CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3 | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / NUCLEOSIDE DIPHOSPHATE KINASE / PHOSPHORYL TRANSFER / BERYLLIUM FLUORIDE | ||||||
Function / homology | Function and homology information 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 / UTP 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 / UTP biosynthetic process / CTP 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 / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xu, Y.W. / Cherfils, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bef.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bef.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bef_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2bef_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2bef_validation.xml.gz | 22 KB | Display | |
Data in CIF | 2bef_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bef ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bef | HTTPS FTP |
-Related structure data
-Links
-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. |
-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.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→15 Å / σ(F): 2
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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: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 20058 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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