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Open data
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Basic information
Entry | Database: PDB / ID: 1un3 | ||||||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T44D | ||||||||||||
![]() | ANGIOGENIN | ||||||||||||
![]() | HYDROLASE / RIBONUCLEASE / NUCLEASE / ENDONUCLEASE / ANGIOGENESIS / PYRROLIDONE CARBOXYLIC ACID | ||||||||||||
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 / homeostatic process ...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 / 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 / rRNA binding / negative regulation of translation / response to hypoxia / 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. / Chavali, G.B. / 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: 1993 Title: Alteration of the Enzymatic Specificity of Human Angiogenin by Site-Directed Mutagenesis Authors: Curran, T.P. / Shapiro, R. / Riordan, J.F. | ||||||||||||
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 | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 353.6 KB | Display | ![]() |
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Full document | ![]() | 353.5 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1un4C ![]() 1un5C ![]() 1b1iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14165.990 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED MUTATION IN CHAIN A, ASP 68 THR (RESIDUE NUMBERING BASED ON SWISSPROT SEQUENCE DATABASE). ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.2 Details: 15% PEG 4000, 0.02% DIOXANE, 0.2M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM CITRATE BUFFER, PH 5.2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.2 / 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: Sep 20, 1999 / Details: RH/SI MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 13959 / % possible obs: 97.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 9.6 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. measured all: 107706 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 9.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B1I Resolution: 1.7→44.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.806 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.109 / 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: 23.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→44.28 Å
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Refine LS restraints |
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