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Yorodumi- PDB-1h52: Binding of Phosphate and Pyrophosphate ions at the active site of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h52 | |||||||||
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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 | 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 / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / 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 / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / homeostatic process / rRNA transcription / activation of phospholipase C activity / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of phosphorylation / RNA endonuclease activity / actin filament polymerization / positive regulation of endothelial cell proliferation / activation of protein kinase B activity / response to hormone / placenta development / negative regulation of smooth muscle cell proliferation / positive regulation of protein secretion / peptide binding / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / heparin binding / chromosome / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / 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: 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 | 1h52.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h52.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1h52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h52 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h52 | HTTPS FTP |
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-Related structure data
Related structure data | 1h53C 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: 14152.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03950 |
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#2: Chemical | ChemComp-POP / |
#3: Water | ChemComp-HOH / |
Compound details | TRNA-SPECIFIC RIBONUCLEA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.02 % | |||||||||||||||||||||||||
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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 ℃ / pH: 5.2 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRRORS |
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→30 Å / Num. obs: 6973 / % possible obs: 91.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2→2.06 Å / % possible all: 78.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 53426 |
Reflection shell | *PLUS % possible obs: 78.4 % |
-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: 0.015 / Data cutoff high absF: 909635.33 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED RESIDUE 1 IS PYROGLUTAMIC ACID WHICH IS NOT ADDED TO THE STRUCTURE AS NO DENSITY WAS OBSERVED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.1265 Å2 / ksol: 0.343749 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 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: 0.053 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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