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- PDB-2yf2: Crystal structure of the oligomerisation domain of C4b-binding pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yf2 | ||||||
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Title | Crystal structure of the oligomerisation domain of C4b-binding protein from Gallus gallus | ||||||
![]() | C4B BINDING PROTEIN | ||||||
![]() | IMMUNE SYSTEM / COMPLEMENT SYSTEM | ||||||
Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3730 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / ACETATE ION / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caesar, J.J.E. / Hill, F. / Lea, S.M. | ||||||
![]() | ![]() Title: Crystal Structure of the Oligomerisation Domain of C4B-Binding Protein from Gallus Gallus Authors: Caesar, J.J.E. / Hill, F. / Lea, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504 KB | Display | ![]() |
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Full document | ![]() | 508.3 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 7304.416 Da / Num. of mol.: 7 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 395-457 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 395 TO SER ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % / Description: NONE |
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Crystal grow | Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE, 8% PEG 3350, PH 4.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→85.46 Å / Num. obs: 23669 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 38.19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 79.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.24→55.06 Å / Cor.coef. Fo:Fc: 0.9068 / Cor.coef. Fo:Fc free: 0.8888 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.193 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 53.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→55.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.34 Å / Total num. of bins used: 12
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