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- PDB-6snk: Crystal structure of the Collagen VI alpha3 N2 domain -

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Basic information

Entry
Database: PDB / ID: 6snk
TitleCrystal structure of the Collagen VI alpha3 N2 domain
ComponentsCollagen alpha-3(VI) chain
KeywordsSTRUCTURAL PROTEIN / collagen VI / von Willebrand factor A domain / alpha/beta Rossmann fold
Function / homology
Function and homology information


collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans ...collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / response to glucose / response to UV / phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix / serine-type endopeptidase inhibitor activity / sarcolemma / extracellular vesicle / collagen-containing extracellular matrix / neuron apoptotic process / cell adhesion / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain ...Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGebauer, J.M. / Degefa, H.S. / Paulsson, M. / Wagener, R. / Baumann, U.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB829 / B11 Germany
German Research FoundationINST 216/682-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of a collagen VI alpha 3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations.
Authors: Solomon-Degefa, H. / Gebauer, J.M. / Jeffries, C.M. / Freiburg, C.D. / Meckelburg, P. / Bird, L.E. / Baumann, U. / Svergun, D.I. / Owens, R.J. / Werner, J.M. / Behrmann, E. / Paulsson, M. / Wagener, R.
History
DepositionAug 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha-3(VI) chain
B: Collagen alpha-3(VI) chain


Theoretical massNumber of molelcules
Total (without water)44,2722
Polymers44,2722
Non-polymers00
Water1,802100
1
A: Collagen alpha-3(VI) chain


Theoretical massNumber of molelcules
Total (without water)22,1361
Polymers22,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagen alpha-3(VI) chain


Theoretical massNumber of molelcules
Total (without water)22,1361
Polymers22,1361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.639, 40.538, 57.114
Angle α, β, γ (deg.)83.342, 76.792, 79.559
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Collagen alpha-3(VI) chain


Mass: 22135.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL6A3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12111
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 30% P550MME_P20K, 0.1M Morpheus buffer 1, 0.12M Morpheus alcohols (condition D1 of Morpheus screen from Molecular Dimensions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→55.4523 Å / Num. obs: 15370 / % possible obs: 96.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.91 Å2 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.147 / Rrim(I) all: 0.267 / Net I/σ(I): 0.939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.273.21.2413410.2250.9031.54696.5
9.07-55.433.30.1462250.9510.0940.17499.1

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Processing

Software
NameVersionClassification
PHENIXdev_3594refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4igi

4igi


Resolution: 2.2→55.43 Å / SU ML: 0.2504 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.3301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 761 4.97 %
Rwork0.2004 14537 -
obs0.2031 15298 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 0 100 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572955
X-RAY DIFFRACTIONf_angle_d0.64813991
X-RAY DIFFRACTIONf_chiral_restr0.0526463
X-RAY DIFFRACTIONf_plane_restr0.0033527
X-RAY DIFFRACTIONf_dihedral_angle_d22.95521083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.29431530.24262881X-RAY DIFFRACTION94.72
2.37-2.610.29851510.23142896X-RAY DIFFRACTION95.61
2.61-2.990.27481490.22332875X-RAY DIFFRACTION95.91
2.99-3.760.26871560.18932952X-RAY DIFFRACTION97
3.76-55.430.21631520.17642933X-RAY DIFFRACTION96.98

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