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Open data
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Basic information
Entry | Database: PDB / ID: 1un5 | ||||||
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Title | ARH-II, AN ANGIOGENIN/RNASE A CHIMERA | ||||||
![]() | ANGIOGENIN | ||||||
![]() | HYDROLASE / PANCREATIC RIBONUCLEASE / ANGIOGENESIS / ANGIOGENIN / CHIMERA / HYBRID / HOMOLOG SCANNING MUTAGENESIS | ||||||
Function / homology | ![]() 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 ...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 / rRNA transcription / : / basement membrane / RNA nuclease activity / positive regulation of phosphorylation / ovarian follicle development / positive regulation of endothelial cell proliferation / RNA endonuclease activity / activation of protein kinase B activity / actin filament polymerization / response to hormone / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / peptide binding / placenta development / antimicrobial humoral immune response mediated by antimicrobial peptide / cell migration / actin cytoskeleton / chromosome / heparin binding / actin binding / growth cone / antibacterial humoral response / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / rRNA binding / negative regulation of translation / response to hypoxia / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holloway, D.E. / Baker, M.D. / Acharya, K.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.3 KB | Display | ![]() |
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PDB format | ![]() | 25.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.6 KB | Display | ![]() |
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Full document | ![]() | 383.3 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1un3C ![]() 1un4C ![]() 2angS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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