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Yorodumi- PDB-2hve: S120G mutant of human nucleoside diphosphate kinase A complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hve | ||||||
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Title | S120G mutant of human nucleoside diphosphate kinase A complexed with ADP | ||||||
Components | Nucleoside diphosphate kinase A | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / S120G MUTANT / COMPLEX ADP | ||||||
Function / homology | Function and homology information DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / positive regulation of DNA binding ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / positive regulation of DNA binding / ribosomal small subunit binding / positive regulation of epithelial cell proliferation / 3'-5' exonuclease activity / lactation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | ||||||
Authors | Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A. | ||||||
Citation | Journal: J.Bioenerg.Biomembr. / Year: 2006 Title: Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP Authors: Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A. #1: Journal: Proteins / Year: 2002 Title: Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor Authors: Min, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W. #2: Journal: J.Mol.Biol. / Year: 2003 Title: Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases Authors: Chen, Y. / Gallois-Montbrun, S. / Schneider, B. / Deville-Bonne, D. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hve.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hve.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hve_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2hve_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2hve_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 2hve_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/2hve ftp://data.pdbj.org/pub/pdb/validation_reports/hv/2hve | HTTPS FTP |
-Related structure data
Related structure data | 2hvdC 1ucnS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17140.693 Da / Num. of mol.: 3 / Mutation: S120G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Plasmid: PET-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase #2: Chemical | #3: 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: 2.9 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.4 M AMMONIUM SULPHATE, 10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.402→40 Å / Num. all: 22088 / Num. obs: 22088 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 49.109 Å2 / Rsym value: 0.1 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.402→2.53 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4 / Rsym value: 0.4 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UCN Resolution: 2.402→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.227 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.111 Å2
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Refinement step | Cycle: LAST / Resolution: 2.402→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.464 Å / Total num. of bins used: 20
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