+Open data
-Basic information
Entry | Database: PDB / ID: 5m9m | |||||||||
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Title | Human angiogenin PD variant Q77P | |||||||||
Components | Angiogenin | |||||||||
Keywords | HYDROLASE / Parkinson's / RNase / angiogenesis | |||||||||
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 / 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 / ovarian follicle development / positive regulation of phosphorylation / RNA endonuclease activity / positive regulation of endothelial cell proliferation / actin filament polymerization / activation of protein kinase B activity / response to hormone / positive regulation of protein secretion / placenta development / negative regulation of smooth muscle cell proliferation / peptide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cell migration / actin cytoskeleton / chromosome / heparin binding / actin binding / growth cone / cytoplasmic vesicle / antibacterial humoral response / endonuclease activity / angiogenesis / negative regulation of translation / rRNA binding / 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 / extracellular region / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Bradshaw, W.J. / Rehman, S. / Pham, T.T.K. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structural insights into human angiogenin variants implicated in Parkinson's disease and Amyotrophic Lateral Sclerosis. Authors: Bradshaw, W.J. / Rehman, S. / Pham, T.T. / Thiyagarajan, N. / Lee, R.L. / 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 | 5m9m.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m9m.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 5m9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/5m9m ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m9m | HTTPS FTP |
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-Related structure data
Related structure data | 5m9aC 5m9cC 5m9gC 5m9jC 5m9pC 5m9qC 5m9rC 5m9sC 5m9tC 5m9vC 1angS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14269.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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-Non-polymers , 5 types, 349 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-BTB / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulphate 0.1 M bis-tris methane 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→56.8 Å / Num. obs: 60548 / % possible obs: 96.6 % / Redundancy: 14.8 % / CC1/2: 0.988 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2326 / CC1/2: 0.622 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANG Resolution: 1.65→56.75 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 2.987 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.922 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→56.75 Å
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