+Open data
-Basic information
Entry | Database: PDB / ID: 8qci | ||||||
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Title | FCGBP D10 Assembly Segment | ||||||
Components | (IgGFc-binding ...) x 2 | ||||||
Keywords | STRUCTURAL PROTEIN / mucus / D assemblies / autocatalytic cleavage / GDPH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yeshaya, N. / Fass, D. | ||||||
Funding support | 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: VWD domain stabilization by autocatalytic Asp-Pro cleavage. Authors: Yeshaya, N. / Gupta, P.K. / Dym, O. / Morgenstern, D. / Major, D.T. / Fass, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qci.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qci.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qci ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qci | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-IgGFc-binding ... , 2 types, 2 molecules BA
#1: Protein | Mass: 29453.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: VWD-C8 segment of the FCGBP D10 assembly; C-terminal cleavage fragment Source: (gene. exp.) Homo sapiens (human) / Gene: FCGBP / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y6R7 |
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#2: Protein/peptide | Mass: 1119.249 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: VWD-C8 segment of the FCGBP D10 assembly; N-terminal cleavage fragment Source: (gene. exp.) Homo sapiens (human) / Gene: FCGBP / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y6R7 |
-Sugars , 1 types, 2 molecules
#3: Sugar |
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-Non-polymers , 3 types, 125 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM Tris, pH 8.0, 22% w/v PEG 8,000, 20% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.34 Å |
Detector | Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Jun 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.49 Å / Num. obs: 16209 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.067 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1567 / CC1/2: 0.599 / Rpim(I) all: 0.509 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.49 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.49 Å
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Refine LS restraints |
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LS refinement shell |
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