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- PDB-6zr3: Crystal structure of tetrameric fibrinogen-like recognition domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zr3 | |||||||||
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Title | Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with N-acetyl-galactosamine-4-sulfate ligand bound | |||||||||
![]() | Fibrinogen C domain-containing protein 1 | |||||||||
![]() | SUGAR BINDING PROTEIN / fibrinogen-like domain / N-acetyl-binding protein | |||||||||
Function / homology | ![]() chitin binding / collagen-containing extracellular matrix / extracellular space / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shrive, A.K. / Greenhough, T.J. / Williams, H.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen associated carbohydrate motifs Authors: Williams, H.M. / Moeller, J.B. / Burns, I. / Schlosser, A. / Sorensen, G.L. / Greenhough, T.J. / Holmskov, U. / Shrive, A.K. #1: ![]() Title: Crystal structure of the tetrameric fibrinogen-like recognition domain of fibrinogen C domain containing 1 (FIBCD1) protein Authors: Shrive, A.K. / Moeller, J.B. / Burns, I. / Paterson, J.M. / Shaw, A.J. / Schlosser, A. / Sorensen, G.L. / Greenhough, T.J. / Holmskov, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zqrC ![]() 6zqxC ![]() 6zqyC ![]() 6zr0C ![]() 6zr4C ![]() 4m7hS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25688.055 Da / Num. of mol.: 2 / Fragment: fibrinogen-like recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/ASG.gif)
#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar | ChemComp-ASG / |
-Non-polymers , 5 types, 242 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-ACY / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % / Mosaicity: 0.3 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.7 M Ammonium Sulphate, 8% Dioxane, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 26, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→53.28 Å / Num. obs: 42961 / % possible obs: 97.3 % / Redundancy: 3.9 % / CC1/2: 0.976 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.056 / Rrim(I) all: 0.118 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 4M7H Resolution: 1.97→53.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.733 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.36 Å2 / Biso mean: 23.457 Å2 / Biso min: 12.06 Å2
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Refinement step | Cycle: final / Resolution: 1.97→53.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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