+Open data
-Basic information
Entry | Database: PDB / ID: 4qfj | ||||||||||||
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Title | The crystal structure of rat angiogenin-heparin complex | ||||||||||||
Components | Angiogenin | ||||||||||||
Keywords | HYDROLASE / catalytic / angiogenesis | ||||||||||||
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: 2.196 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 | 4qfj.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qfj.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qfj_validation.pdf.gz | 863.9 KB | Display | wwPDB validaton report |
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Full document | 4qfj_full_validation.pdf.gz | 869.4 KB | Display | |
Data in XML | 4qfj_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4qfj_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qfj ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfj | HTTPS FTP |
-Related structure data
Related structure data | 4qfiC 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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1 |
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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: Polysaccharide | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 9% PEG8000, 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-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.196→50 Å / Num. obs: 13833 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.196→2.24 Å / % possible all: 99.9 |
-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: 2.196→38.189 Å / SU ML: 0.63 / σ(F): 1.35 / Phase error: 25.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.091 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.196→38.189 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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