+Open data
-Basic information
Entry | Database: PDB / ID: 1pae | ||||||
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Title | nucleoside diphosphate kinase | ||||||
Components | Nucleoside diphosphate kinase, cytosolicNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / selenocysteine selenomethionine | ||||||
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 / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Strub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing Authors: Strub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C. #1: Journal: Structure / Year: 2002 Title: Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein. Authors: Sanchez, J.-F. / Hoh, F. / Strub, M.-P. / Aumelas, A. / Dumas, C. | ||||||
History |
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Remark 600 | HETEROGEN THE HETATM ENTRY SE 121 CORRESPONDS TO A SELENOCYSTEINE ADDUCT TO SEC 122 (NOT VISIBLE IN ...HETEROGEN THE HETATM ENTRY SE 121 CORRESPONDS TO A SELENOCYSTEINE ADDUCT TO SEC 122 (NOT VISIBLE IN THE ELECTRON DENSITY MAP EXCEPT SELENIUM ATOM) WITH A DISELENIDE BRIDGE BETWEEN SE 121 AND SE SEC X 122 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pae.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pae.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/1pae ftp://data.pdbj.org/pub/pdb/validation_reports/pa/1pae | HTTPS FTP |
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-Related 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: 16968.912 Da / Num. of mol.: 1 / Mutation: H122C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: ndk / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) selB::kan Cys51E / References: UniProt: P22887, nucleoside-diphosphate kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, magnesium chloride,Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9754 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2003 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9754 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→24.71 Å / Num. all: 5418 / Num. obs: 5418 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.7→2.77 Å / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Num. measured all: 114811 |
Reflection shell | *PLUS Lowest resolution: 2.74 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→24.71 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.98 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.486 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.258 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→24.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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