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Yorodumi- PDB-6zr0: Crystal structure of tetrameric fibrinogen-like recognition domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zr0 | ||||||
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Title | Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with N-acetylalanine ligand bound | ||||||
Components | Fibrinogen C domain-containing protein 1 | ||||||
Keywords | SUGAR BINDING PROTEIN / fibrinogen-like domain / N-acetyl-binding protein | ||||||
Function / homology | Function and homology information chitin binding / collagen-containing extracellular matrix / extracellular space / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Shrive, A.K. / Greenhough, T.J. / Williams, H.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 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: Journal: J Biol Chem / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zr0.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zr0.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zr0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6zr0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6zr0_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6zr0_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/6zr0 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/6zr0 | HTTPS FTP |
-Related structure data
Related structure data | 6zqrC 6zqxC 6zqyC 6zr3C 6zr4C 4m7hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.21252/zcfy-cw20 / Data set type: diffraction image data / Details: https://doi.org/10.21252/zcfy-cw20 |
-Links
-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 / Sugars , 2 types, 3 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.) Homo sapiens (human) / Gene: FIBCD1, UNQ701/PRO1346 / Plasmid: pNT-Bac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N539 #2: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
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-Non-polymers , 6 types, 259 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.06 Å3/Da / Density % sol: 59.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→84.44 Å / Num. obs: 46069 / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.401 / Num. unique obs: 3105 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 4M7H Resolution: 1.94→84.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.109 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.123 / 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: 62.83 Å2 / Biso mean: 21.69 Å2 / Biso min: 12.45 Å2
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Refinement step | Cycle: final / Resolution: 1.94→84.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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