+Open data
-Basic information
Entry | Database: PDB / ID: 1jxv | ||||||
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Title | Crystal Structure of Human Nucleoside Diphosphate Kinase A | ||||||
Components | Nucleoside Diphosphate Kinase A | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding / positive regulation of DNA binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / phosphorylation / 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: 2.2 Å | ||||||
Authors | Min, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary X-ray crystallographic analysis of human nucleoside diphosphate kinase A Authors: Min, K. / Kim, S.Y. / Song, H.K. / Chang, C. / Cho, S.J. / Moon, J. / Yang, J.K. / Lee, J.Y. / Lee, K.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxv.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxv.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jxv_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 1jxv_full_validation.pdf.gz | 479 KB | Display | |
Data in XML | 1jxv_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 1jxv_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxv ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxv | HTTPS FTP |
-Related structure data
Related structure data | 1nueS 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: 17170.721 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: nm23-H1 / Plasmid: pET-3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15531, nucleoside-diphosphate kinase #2: 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: 2.27 Å3/Da / Density % sol: 45.81 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: MPD, MES-KOH, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 288 K | ||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 48679 / % possible obs: 90.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.1 |
Reflection | *PLUS Lowest resolution: 50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NUE Resolution: 2.2→6 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / Rfactor obs: 0.207 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |