+Open data
-Basic information
Entry | Database: PDB / ID: 4qfi | ||||||
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Title | The crystal structure of rat angiogenin-heparin complex | ||||||
Components | Angiogenin | ||||||
Keywords | HYDROLASE / catalytic / angiogenesis / Heparin | ||||||
Function / homology | Function and homology information tRNA destabilization / tRNA-specific ribonuclease activity / protein kinase C signaling / cell growth involved in cardiac muscle cell development / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / response to yeast / antifungal humoral response / cardiac muscle hypertrophy ...tRNA destabilization / tRNA-specific ribonuclease activity / protein kinase C signaling / cell growth involved in cardiac muscle cell development / activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / response to yeast / antifungal humoral response / cardiac muscle hypertrophy / renal absorption / rRNA transcription / basement membrane / RNA nuclease activity / positive regulation of phosphorylation / positive regulation of endothelial cell proliferation / actin filament polymerization / response to hormone / liver development / angiotensin-activated signaling pathway / positive regulation of protein secretion / cellular response to glucose stimulus / negative regulation of smooth muscle cell proliferation / peptide binding / cellular response to mechanical stimulus / antimicrobial humoral immune response mediated by antimicrobial peptide / cell migration / antibacterial humoral response / heparin binding / actin binding / gene expression / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / response to hypoxia / defense response to Gram-positive bacterium / positive regulation of protein phosphorylation / copper ion binding / innate immune response / signaling receptor binding / neuronal cell body / nucleolus / protein homodimerization activity / extracellular space / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 Å | ||||||
Authors | Yeo, K.J. / Hwang, E. / Min, K.M. / Hwang, K.Y. / Jeon, Y.H. / Chang, S.I. / Cheong, H.K. | ||||||
Citation | Journal: To be Published Title: The crystal structure of rat angiogenin-heparin complex Authors: Yeo, K.J. / Hwang, E. / Min, K.M. / Hwang, K.Y. / Jeon, Y.H. / Chang, S.I. / Cheong, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qfi.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qfi.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qfi_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 4qfi_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 4qfi_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4qfi_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qfi ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfi | HTTPS FTP |
-Related structure data
Related structure data | 4qfjC 2bwkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14042.957 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 24-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ang, Ang1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5WRG2 #2: Chemical | #3: Chemical | ChemComp-ACY / #4: 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: 2.58 Å3/Da / Density % sol: 52.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 24% PEG 8,000, 5mM zinc acetate, 100mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 28081 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.78→1.83 Å / % possible all: 98.5 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BWK Resolution: 1.784→33.302 Å / SU ML: 0.22 / σ(F): 1.46 / Phase error: 24.38 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.784→33.302 Å
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Refine LS restraints |
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LS refinement shell |
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