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Yorodumi- PDB-3bbf: Crystal structure of the NM23-H2 transcription factor complex with GDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bbf | ||||||
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Title | Crystal structure of the NM23-H2 transcription factor complex with GDP | ||||||
Components | Nucleoside diphosphate kinase B | ||||||
Keywords | TRANSFERASE / transcription factor / cancer / kinase / nm23 gen / hexamer / Activator / Anti-oncogene / ATP-binding / Cell cycle / DNA-binding / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Nucleus / Phosphorylation / Transcription regulation | ||||||
Function / homology | Function and homology information regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / histidine kinase / ruffle / cell periphery / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / GDP binding / lamellipodium / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: Mol.Cancer Ther. / Year: 2009 Title: NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1. Authors: Dexheimer, T.S. / Carey, S.S. / Zuohe, S. / Gokhale, V.M. / Hu, X. / Murata, L.B. / Maes, E.M. / Weichsel, A. / Sun, D. / Meuillet, E.J. / Montfort, W.R. / Hurley, L.H. #1: Journal: Structure / Year: 1995 Title: X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution. Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bbf.cif.gz | 210.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bbf.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbf_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3bbf_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3bbf_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 3bbf_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbf ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbf | HTTPS FTP |
-Related structure data
Related structure data | 3bbbC 3bbcC 1nueS S: Starting model for refinement C: citing same article (ref.) |
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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: 17192.859 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P22392, nucleoside-diphosphate kinase #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #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: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1500, 50 mM Tris-HCl, 200 mM MgCl2, 2 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1271 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2004 / Details: bent Si-mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 103223 / Num. obs: 103223 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.3 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1NUE Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.406 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.833 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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