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Yorodumi- PDB-3zxc: E69 deletion mutant single insulin-like growth factor binding dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zxc | ||||||
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Title | E69 deletion mutant single insulin-like growth factor binding domain protein (SIBD-1) from Cupiennius salei | ||||||
Components | SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1 | ||||||
Keywords | SIGNALING / IGFBP / SINGLE INSULIN-BINDING DOMAIN | ||||||
Function / homology | Function and homology information insulin-like growth factor binding / regulation of cell growth / innate immune response / extracellular region Similarity search - Function | ||||||
Biological species | CUPIENNIUS SALEI (spider) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Widmer, C. / Baumann, U. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Structural and Biochemical Characterization of Native and Recombinant Single Insulin-Like Growth Factor-Binding Domain Protein (Sibd-1) from the Central American Hunting Spider Cupiennius Salei (Ctenidae). Authors: Trachsel, C. / Widmer, C. / Kampfer, U. / Buhr, C. / Baumann, T. / Kuhn-Nentwig, L. / Schurch, S. / Schaller, J. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zxc.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zxc.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zxc_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 3zxc_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 3zxc_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3zxc_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxc ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxc | HTTPS FTP |
-Related 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: 8038.088 Da / Num. of mol.: 2 Fragment: INSULIN-LIKE GROWTH FACTOR BINDING DOMAIN RESIDUES 20-97 Source method: isolated from a genetically manipulated source Details: E69 DELETION MUTANT / Source: (gene. exp.) CUPIENNIUS SALEI (spider) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4V4F9 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 2.2 M SODIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. obs: 34438 / % possible obs: 98.6 % / Observed criterion σ(I): 2.16 / Redundancy: 5.7 % / Biso Wilson estimate: 17.76 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.16 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.4→35.007 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 19.31 / Stereochemistry target values: ML Details: RESIDUES 61-66 IN CHAIN A, 64-67 IN CHAIN B ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.16 Å2 / ksol: 0.457 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.4→35.007 Å
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Refine LS restraints |
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LS refinement shell |
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