+Open data
-Basic information
Entry | Database: PDB / ID: 1un5 | ||||||
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Title | ARH-II, AN ANGIOGENIN/RNASE A CHIMERA | ||||||
Components | ANGIOGENIN | ||||||
Keywords | HYDROLASE / PANCREATIC RIBONUCLEASE / ANGIOGENESIS / ANGIOGENIN / CHIMERA / HYBRID / HOMOLOG SCANNING MUTAGENESIS | ||||||
Function / homology | Function and homology information activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / : / oocyte maturation ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / : / oocyte maturation / pancreatic ribonuclease / ribonuclease A activity / homeostatic process / positive regulation of phosphorylation / rRNA transcription / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of endothelial cell proliferation / RNA endonuclease activity / actin filament polymerization / activation of protein kinase B activity / negative regulation of smooth muscle cell proliferation / response to hormone / peptide binding / placenta development / positive regulation of protein secretion / chromosome / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / cell migration / heparin binding / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / response to hypoxia / rRNA binding / negative regulation of translation / lyase activity / defense response to Gram-positive bacterium / copper ion binding / innate immune response / signaling receptor binding / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Holloway, D.E. / Baker, M.D. / Acharya, K.R. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystallographic Studies on Structural Features that Determine the Enzymatic Specificity and Potency of Human Angiogenin: Thr44, Thr80 and Residues 38-41 Authors: Holloway, D.E. / Chavali, G.B. / Hares, M.C. / Baker, M.D. / Subbarao, G.V. / Shapiro, R. / Acharya, K.R. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Refined Crystal Structures of Native Human Angiogenin and Two Active Site Variants: Implications for the Unique Functional Properties of an Enzyme Involved in Neovascularisation During Tumour Growth Authors: Leonidas, D.D. / Shapiro, R. / Allen, S.C. / Subbarao, G.V. / Veluraja, K. / Acharya, K.R. #2: Journal: Biochemistry / Year: 1990 Title: Mutagenesis of Residues Flanking Lys-40 Enhances the Enzymatic Activity and Reduces the Angiogenic Potency of Angiogenin Authors: Harper, J.W. / Fox, E.A. / Shapiro, R. / Vallee, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1un5.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1un5.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1un5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1un5_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
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Full document | 1un5_full_validation.pdf.gz | 383.3 KB | Display | |
Data in XML | 1un5_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1un5_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1un5 ftp://data.pdbj.org/pub/pdb/validation_reports/un/1un5 | HTTPS FTP |
-Related structure data
Related structure data | 1un3C 1un4C 2angS 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: 14457.428 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 38-42 IN THE COORDINATES ARE FROM BOVINE PANCREATIC RIBONUCLEASE A Source: (gene. exp.) HOMO SAPIENS (human) / Description: GUEST SEGMENT IS BOVINE. SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P03950, UniProt: P00656, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Compound details | REPLACEMENT OF ANGIOGENIN 62-65 WITH RIBONUCLEASE A 64-68. (RESIDUE NUMBERING BASED ON SWISSPROT ...REPLACEMEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 Details: 10% PEG 6000, PH 5.4 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / 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: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 4, 2002 / Details: RH/SI MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 5767 / % possible obs: 95.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.6→2.66 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 8.3 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. measured all: 35002 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 8.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ANG Resolution: 2.6→67.42 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.954 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.273 / 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: 52.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→67.42 Å
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Refine LS restraints |
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