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Yorodumi- PDB-1agi: CRYSTAL STRUCTURE OF BOVINE ANGIOGENIN AT 1.5 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1agi | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE ANGIOGENIN AT 1.5 ANGSTROMS RESOLUTION | ||||||
Components | ANGIOGENIN | ||||||
Keywords | ENDONUCLEASE | ||||||
Function / homology | Function and homology information activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription / : / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of endothelial cell proliferation ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / rRNA transcription / : / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of endothelial cell proliferation / actin filament polymerization / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / cell differentiation / response to hypoxia / negative regulation of translation / defense response to Gram-positive bacterium / copper ion binding / innate immune response / signaling receptor binding / neuronal cell body / nucleolus / DNA binding / extracellular space / nucleus Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Acharya, K.R. / Shapiro, R. / Riordan, J.F. / Vallee, B.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Crystal structure of bovine angiogenin at 1.5-A resolution. Authors: Acharya, K.R. / Shapiro, R. / Riordan, J.F. / Vallee, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1agi.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1agi.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 1agi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agi_validation.pdf.gz | 362.8 KB | Display | wwPDB validaton report |
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Full document | 1agi_full_validation.pdf.gz | 363.9 KB | Display | |
Data in XML | 1agi_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1agi_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agi ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 39 / 2: CIS PROLINE - PRO 92 |
-Components
#1: Protein | Mass: 14621.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: MILK References: UniProt: P10152, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 43 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→8 Å / Num. obs: 17940 / % possible obs: 87 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. obs: 18103 / Num. measured all: 149878 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / Highest resolution: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 17940 / σ(I): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |