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Yorodumi- PDB-4b36: Crystal Structure of Human Angiogenin with an Engineered Loop Exh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b36 | ||||||
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Title | Crystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule | ||||||
Components | ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN | ||||||
Keywords | HYDROLASE / EDN / ANG / ANTIVIRAL / ANGIOGENESIS / TUMOR / AMYOTROPHIC LATERAL SCLEROSIS / PARKINSONS DISEASE | ||||||
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 / peptide binding / negative regulation of smooth muscle cell proliferation / placenta development / antimicrobial humoral immune response mediated by antimicrobial peptide / cell migration / actin cytoskeleton / chromosome / heparin binding / actin binding / growth cone / antibacterial humoral response / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / 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: 1.76 Å | ||||||
Authors | Thiyagarajan, N. / Acharya, K.R. | ||||||
Citation | Journal: FEBS Open Bio. / Year: 2012 Title: Crystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule Authors: Thiyagarajan, N. / 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 | 4b36.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b36.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 4b36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b36_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 4b36_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 4b36_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4b36_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b36 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b36 | HTTPS FTP |
-Related structure data
Related structure data | 1angS 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: 14523.436 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-107,111-120,116-147 Source method: isolated from a genetically manipulated source Details: IN THIS STUDY WE HAVE SUBSTITUTED 84- HGGSPWPP-91 OF ANG WITH 86-TTPSPQNISN-95 OF EOSINOPHIL- DERIVED NEUROTOXIN AND CONSTRUCTED AN ANG-EDN HYBRID Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIPL References: UniProt: P03950, UniProt: Q12762, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | IN THIS STUDY WE HAVE SUBSTITUTED 84-HGGSPWPP-91 OF ANG WITH 86-TTPSPQNISN-95 OF EOSINOPHIL-DERIVED ...IN THIS STUDY WE HAVE SUBSTITUTE | |
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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: 1.81 Å3/Da / Density % sol: 32.2 % / Description: NONE |
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Crystal grow | Details: 1.75-2.5 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 20481 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 27.12 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / % possible all: 65.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ANG Resolution: 1.76→20.151 Å / SU ML: 0.18 / σ(F): 0.1 / Phase error: 28.23 / 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 / Bsol: 58.578 Å2 / ksol: 0.427 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.76→20.151 Å
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Refine LS restraints |
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LS refinement shell |
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