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- PDB-6s4c: Crystal Structure of the vWFA2 subdomain of type VII collagen -

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Basic information

Entry
Database: PDB / ID: 6s4c
TitleCrystal Structure of the vWFA2 subdomain of type VII collagen
ComponentsCollagen alpha-1(VII) chain
KeywordsSTRUCTURAL PROTEIN / vWFA / collagen VII / VWA
Function / homology
Function and homology information


Anchoring fibril formation / Extracellular matrix organization / Laminin interactions / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / Cargo concentration in the ER / COPII-mediated vesicle transport / Integrin cell surface interactions ...Anchoring fibril formation / Extracellular matrix organization / Laminin interactions / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / Cargo concentration in the ER / COPII-mediated vesicle transport / Integrin cell surface interactions / collagen trimer / basement membrane / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / cell adhesion / extracellular space / extracellular region / identical protein binding
Similarity search - Function
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. / 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 ...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. / 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 / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-EDT / PHOSPHATE ION / Collagen alpha-1(VII) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGebauer, J.M. / Flachsenberg, F. / Baumann, U. / Seeger, K.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB829 Germany
German Research FoundationEXC 306 Germany
German Research FoundationRTG1727 Germany
CitationJournal: Febs Open Bio / Year: 2020
Title: Structural and biophysical characterization of the type VII collagen vWFA2 subdomain leads to identification of two binding sites.
Authors: Gebauer, J.M. / Flachsenberg, F. / Windler, C. / Richer, B. / Baumann, U. / Seeger, K.
History
DepositionJun 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(VII) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2425
Polymers20,8061
Non-polymers4364
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-20 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.034, 123.034, 63.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1301-

MG

21A-1304-

PO4

31A-1304-

PO4

41A-1401-

HOH

51A-1406-

HOH

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Components

#1: Protein Collagen alpha-1(VII) chain / Long-chain collagen / LC collagen


Mass: 20805.834 Da / Num. of mol.: 1 / Fragment: VWFA2 SUBDOMAIN (UNP RESIDUES 1048-1238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Col7a1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63870
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.8 M mangesium sulphate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2→35.52 Å / Num. obs: 12575 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 923 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
ARP/wARPmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX1.9_1685refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGI

4igi


Resolution: 2→35.52 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.83
RfactorNum. reflection% reflectionSelection details
Rfree0.207 626 4.98 %Random selection
Rwork0.176 ---
obs0.178 12573 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.99 Å2
Refinement stepCycle: LAST / Resolution: 2→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 17 140 1547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031457
X-RAY DIFFRACTIONf_angle_d0.7551990
X-RAY DIFFRACTIONf_dihedral_angle_d11.645557
X-RAY DIFFRACTIONf_chiral_restr0.029234
X-RAY DIFFRACTIONf_plane_restr0.004267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.20130.23321660.23012940X-RAY DIFFRACTION100
2.2013-2.51980.25641560.2022966X-RAY DIFFRACTION100
2.5198-3.17440.23661550.18132976X-RAY DIFFRACTION100
3.1744-35.52240.16771490.15093065X-RAY DIFFRACTION100

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