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Open data
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Basic information
Entry | Database: PDB / ID: 3pon | ||||||
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Title | Crystal structure of MBL collagen-like peptide | ||||||
![]() | MBL collagen-like peptide | ||||||
![]() | UNKNOWN FUNCTION / Collagen peptide / MBL collagen-like region / Complement protein / lectin pathway of complement / MASPs (MASP-1 to 3) CUB1 and CUB2 domains / Bloodstream | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gingras, A.R. / Moody, P.C.E. / Wallis, R. | ||||||
![]() | ![]() Title: Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation. Authors: Gingras, A.R. / Girija, U.V. / Keeble, A.H. / Panchal, R. / Mitchell, D.A. / Moody, P.C. / Wallis, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pobC ![]() 3podSC ![]() 3poeC ![]() 3pofC ![]() 3pogC ![]() 3poiC ![]() 3pojC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2479.700 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic peptide #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.6M Ammonium Sulphate, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2010 / Details: focusing mirrors |
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→23.485 Å / Num. obs: 8744 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2 / Num. unique all: 3561 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3POD Resolution: 1.5→21.26 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.707 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→21.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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