+Open data
-Basic information
Entry | Database: PDB / ID: 1b4s | ||||||
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Title | STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / TRANSFERASE / KINASE / ATP-BINDING | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Meyer, P. / Janin, J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 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: Journal: Biochemistry / Year: 1995 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: Journal: Biochemistry / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b4s.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4s.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b4s_validation.pdf.gz | 563.1 KB | Display | wwPDB validaton report |
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Full document | 1b4s_full_validation.pdf.gz | 575.6 KB | Display | |
Data in XML | 1b4s_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1b4s_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4s ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4s | HTTPS FTP |
-Related structure data
Related structure data | 1kdnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) 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: 2.14 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: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 7.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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