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Open data
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Basic information
Entry | Database: PDB / ID: 1b4s | ||||||
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Title | STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | PHOSPHOTRANSFERASE / TRANSFERASE / KINASE / ATP-BINDING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Meyer, P. / Janin, J. | ||||||
![]() | ![]() Title: Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase. Authors: Admiraal, S.J. / Schneider, B. / Meyer, P. / Janin, J. / Veron, M. / Deville-Bonne, D. / Herschlag, D. #1: ![]() Title: Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium Authors: Morera, S. / Chiadmi, M. / Lebras, G. / Lascu, I. / Janin, J. #2: ![]() Title: Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase Authors: Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Briozzo, P. / Veron, M. / Janin, 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 | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 563.1 KB | Display | ![]() |
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Full document | ![]() | 575.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kdnS S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16735.242 Da / Num. of mol.: 3 / Mutation: H122G Source method: isolated from a genetically manipulated source 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: 2.14 Å3/Da / Density % sol: 42.44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→8 Å / Num. obs: 14555 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Num. obs: 15492 / Num. measured all: 150824 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rmerge(I) obs: 0.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KDN Resolution: 2.5→8 Å / σ(F): 2 Details: MUTANT HAS LOST NDPK ACTIVITY, BUT EFFICIENTLY PHOSPHORYLATES IMIDAZOLE AND OTHER PHOSPHATE ACCEPTOR MOLECULES (AMINES AND ALCOHOLS). THE PROTEIN WAS CRYSTALLIZED WITH ATP, BUT THE ...Details: MUTANT HAS LOST NDPK ACTIVITY, BUT EFFICIENTLY PHOSPHORYLATES IMIDAZOLE AND OTHER PHOSPHATE ACCEPTOR MOLECULES (AMINES AND ALCOHOLS). THE PROTEIN WAS CRYSTALLIZED WITH ATP, BUT THE NUCLEOTIDE IS SEEN TO BE HYDROLYZED TO ADP+PO4 IN THE CRYSTAL.
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Displacement parameters | Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 7.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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