+Open data
-Basic information
Entry | Database: PDB / ID: 2bwl | ||||||
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Title | Murine angiogenin, phosphate complex | ||||||
Components | ANGIOGENIN | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / ANGIOGENESIS / CANCER | ||||||
Function / homology | Function and homology information tRNA destabilization / tRNA-specific ribonuclease activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Adherens junctions interactions / response to yeast / antifungal humoral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription ...tRNA destabilization / tRNA-specific ribonuclease activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Adherens junctions interactions / response to yeast / antifungal humoral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription / activation of phospholipase C activity / basement membrane / RNA nuclease activity / positive regulation of phosphorylation / actin filament polymerization / positive regulation of endothelial cell proliferation / response to hormone / central nervous system development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / peptide binding / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / heparin binding / chromosome / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / cell differentiation / response to hypoxia / defense response to Gram-positive bacterium / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Holloway, D.E. / Chavali, G.B. / Hares, M.C. / Subramanian, V. / Acharya, K.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Murine Angiogenin: Features of the Substrate- and Cell-Binding Regions and Prospects for Inhibitor-Binding Studies. Authors: Holloway, D.E. / Chavali, G.B. / Hares, M.C. / Subramanian, V. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bwl.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bwl.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/2bwl ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bwl | HTTPS FTP |
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-Related structure data
Related structure data | 2bwkC 1agiS 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
#1: Protein | Mass: 13792.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Plasmid: PMANG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P21570, EC: 3.1.27.5 | ||
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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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 5.2 / Details: 25% PEG 4000, 0.1M SODIUM PHOSPHATE BUFFER, PH 5.2 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 9, 2000 |
Radiation | Monochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 16648 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4 / % possible all: 61.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AGI Resolution: 1.62→42.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.057 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / 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: 19.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→42.33 Å
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Refine LS restraints |
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