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- PDB-8qci: FCGBP D10 Assembly Segment -

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Basic information

Entry
Database: PDB / ID: 8qci
TitleFCGBP D10 Assembly Segment
Components(IgGFc-binding ...) x 2
KeywordsSTRUCTURAL PROTEIN / mucus / D assemblies / autocatalytic cleavage / GDPH
Function / homology
Function and homology information


extracellular matrix / extracellular space / extracellular exosome
Similarity search - Function
IgGFc-binding protein, N-terminal / IgGFc binding protein / TILa domain / TILa domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 ...IgGFc-binding protein, N-terminal / IgGFc binding protein / TILa domain / TILa domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor (vWF) type C domain / VWFC domain / Epidermal growth factor-like domain. / EGF-like domain
Similarity search - Domain/homology
IgGFc-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYeshaya, N. / Fass, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionAug 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: IgGFc-binding protein
A: IgGFc-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1476
Polymers30,5722
Non-polymers5754
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-1 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.716, 54.321, 129.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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IgGFc-binding ... , 2 types, 2 molecules BA

#1: Protein IgGFc-binding protein / VWD-C8 segment of the FCGBP D10 assembly / C-terminal cleavage fragment


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
#2: Protein/peptide IgGFc-binding protein / VWD-C8 segment of the FCGBP D10 assembly / N-terminal cleavage fragment


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

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 125 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.34 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2565 1133 7 %
Rwork0.1963 --
obs0.2005 16192 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 35 123 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092204
X-RAY DIFFRACTIONf_angle_d0.8973026
X-RAY DIFFRACTIONf_dihedral_angle_d6.28323
X-RAY DIFFRACTIONf_chiral_restr0.057337
X-RAY DIFFRACTIONf_plane_restr0.01396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.41541380.33091834X-RAY DIFFRACTION99
2.3-2.420.30561380.23911845X-RAY DIFFRACTION100
2.42-2.570.29721420.21541871X-RAY DIFFRACTION100
2.57-2.770.28111380.1991844X-RAY DIFFRACTION100
2.77-3.050.26981420.20081878X-RAY DIFFRACTION100
3.05-3.490.25671420.1871885X-RAY DIFFRACTION100
3.49-4.380.21831440.17081915X-RAY DIFFRACTION100
4.39-19.490.21611490.17341987X-RAY DIFFRACTION99

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