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Open data
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Basic information
Entry | Database: PDB / ID: 1a4y | ||||||
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Title | RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX | ||||||
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![]() | COMPLEX (INHIBITOR/NUCLEASE) / COMPLEX (INHIBITOR-NUCLEASE) / COMPLEX (RI-ANG) / HYDROLASE MOLECULAR RECOGNITION / EPITOPE MAPPING / LEUCINE-RICH REPEATS / COMPLEX (INHIBITOR-NUCLEASE) complex | ||||||
Function / homology | ![]() ribonuclease inhibitor activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / regulation of Arp2/3 complex-mediated actin nucleation / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions ...ribonuclease inhibitor activity / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / regulation of Arp2/3 complex-mediated actin nucleation / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / mRNA catabolic process / rRNA transcription / : / basement membrane / RNA nuclease activity / regulation of angiogenesis / 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 / lamellipodium / chromosome / heparin binding / actin binding / growth cone / antibacterial humoral response / regulation of inflammatory 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 exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Papageorgiou, A.C. / Acharya, K.R. | ||||||
![]() | ![]() Title: Molecular recognition of human angiogenin by placental ribonuclease inhibitor--an X-ray crystallographic study at 2.0 A resolution. Authors: Papageorgiou, A.C. / Shapiro, R. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.7 KB | Display | ![]() |
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PDB format | ![]() | 181.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.7 KB | Display | ![]() |
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Full document | ![]() | 421 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bnh 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.63908, 0.58117, 0.50381), Vector: Details | THERE ARE TWO COMPLEXES IN THE ASYMMETRIC UNIT (CHAINS A, B, C AND D, E, F). CHAINS A AND D CORRESPOND TO THE INHIBITOR, CHAINS B AND E CORRESPOND TO ANGIOGENIN, AND CHAINS C AND F CORRESPOND TO THE WATER MOLECULES ASSOCIATED WITH THE RESPECTIVE COMPLEX. | |
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Components
#1: Protein | Mass: 49887.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): W3110 / References: UniProt: P13489 #2: Protein | Mass: 14169.036 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): W3110 References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.82 % Description: THE POSITION OF ANGIOGENIN WAS LOCATED BY EXAMINATION OF THE ELECTRON DENSITY MAP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.2 Details: THE COMPLEX WAS CRYSTALLIZED FROM 10% PEG4000, 20MM SODIUM CITRATE (PH 4.2), 0.1 AMMONIUM SULPHATE AND 25 MM DTT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 | |||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→40 Å / Num. obs: 72355 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 4.5 | |||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.6 / % possible all: 65.4 | |||||||||
Reflection | *PLUS Num. measured all: 158593 | |||||||||
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 65.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNH (PIG RIBONUCLEASE INHIBITOR) ![]() 1bnh Resolution: 2→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a free: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42 Å2 |