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Yorodumi- PDB-1h53: Binding of Phosphate and Pyrophosphate ions at the active site of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h53 | |||||||||
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Title | Binding of Phosphate and Pyrophosphate ions at the active site of human Angiogenin as revealed by X-ray Crystallography | |||||||||
Components | ANGIOGENIN | |||||||||
Keywords | HYDROLASE / ANGIOGENIN / RIBONUCLEASE / PHOSPHATE / PYROPHOSPHATE | |||||||||
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 / 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 / actin cytoskeleton / cell migration / chromosome / heparin binding / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / endonuclease activity / angiogenesis / 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 | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Leonidas, D.D. / Chavali, G.B. / Jardine, A.M. / Li, S. / Shapiro, R. / Acharya, K.R. | |||||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Binding of Phosphate and Pyrophosphate Ions at the Active Site of Human Angiogenin as Revealed by X-Ray Crystallography Authors: Leonidas, D.D. / Chavali, G.B. / Jardine, A.M. / Li, S. / Shapiro, R. / Acharya, K.R. #1: Journal: J.Mol.Biol. / Year: 1999 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. / Velouraja, K. / 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 | 1h53.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h53.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h53_validation.pdf.gz | 392.2 KB | Display | wwPDB validaton report |
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Data in XML | 1h53_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1h53_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h53 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h53 | HTTPS FTP |
-Related structure data
Related structure data | 1h52C 1hbyC 1b1iS 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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Unit cell |
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-Components
#1: Protein | Mass: 14080.930 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Compound details | TRNA-SPECIFIC RIBONUCLEASE THAT BINDS TO ACTIN ON THE SURFACE OF ENDOTHELIAL CELLS CHAIN A ...TRNA-SPECIFIC RIBONUCLEA |
Sequence details | THE N-TERMINAL RESIDUE (PCA 1) IS A PYROGLUTAM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % | ||||||||||||||||||||
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Crystal grow | pH: 5.2 Details: 20MM SODIUM CITRATE, 0.2M SODIUM POTASSIUM TARTARATE, 10% PEG 6000 PH 5.2 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.87 |
Detector | Date: Sep 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 8677 / % possible obs: 97.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.06 Å / % possible all: 85.6 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 45669 / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 85.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B1I Resolution: 2→20 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED RESIDUES 1 AND 2 ARE DISORDERED AND WERE NOT ADDED TO THE FILE
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Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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