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Yorodumi- PDB-4ahl: P112L - Angiogenin mutants and amyotrophic lateral sclerosis - a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ahl | ||||||
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Title | P112L - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis | ||||||
Components | ANGIOGENIN | ||||||
Keywords | HYDROLASE / NEOVASCULARISATION | ||||||
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 / 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 / response to hypoxia / rRNA binding / negative regulation of translation / 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: 2.053 Å | ||||||
Authors | Thiyagarajan, N. / Ferguson, R. / Saha, S. / Pham, T. / Subramanian, V. / Acharya, K.R. | ||||||
Citation | Journal: Nat.Commun. / Year: 2012 Title: Structural and Molecular Insights Into the Mechanism of Action of Human Angiogenin-Als Variants in Neurons. Authors: Thiyagarajan, N. / Ferguson, R. / 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 | 4ahl.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ahl.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ahl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ahl_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 4ahl_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 4ahl_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 4ahl_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/4ahl ftp://data.pdbj.org/pub/pdb/validation_reports/ah/4ahl | HTTPS FTP |
-Related structure data
Related structure data | 4ahdC 4aheC 4ahfC 4ahgC 4ahhC 4ahiC 4ahjC 4ahkC 4ahmC 4ahnC 4aohC 1angS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14185.079 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B(PLUS) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS - RIPL References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.1 % / Description: NONE |
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Crystal grow | Details: 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 9350 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 25.98 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 60.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ANG Resolution: 2.053→25.44 Å / SU ML: 0.31 / σ(F): 0.04 / Phase error: 31.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.569 Å2 / ksol: 0.479 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.053→25.44 Å
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Refine LS restraints |
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LS refinement shell |
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