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- PDB-4ihk: Crystal structure of the Collagen VI alpha3 N5 domain R1061Q -

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Basic information

Entry
Database: PDB / ID: 4ihk
TitleCrystal structure of the Collagen VI alpha3 N5 domain R1061Q
ComponentsCollagen alpha3(VI)
KeywordsCELL ADHESION / Collagen VI 3N5 / VWA
Function / homology
Function and homology information


NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / ECM proteoglycans / Integrin cell surface interactions / collagen trimer / response to glucose ...NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / ECM proteoglycans / Integrin cell surface interactions / collagen trimer / response to glucose / response to UV / phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix / serine-type endopeptidase inhibitor activity / sarcolemma / collagen-containing extracellular matrix / neuron apoptotic process / cell adhesion / extracellular space
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / : / von Willebrand factor, 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. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain ...Collagen alpha-3(VI) chain, vWA domain / : / von Willebrand factor, 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. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Collagen, type VI, alpha 3 / Collagen alpha3(VI)
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMikolajek, H. / Becker, A.K.A. / Paulsson, M. / Wagener, R. / Werner, J.M.
CitationJournal: Structure / Year: 2014
Title: A structure of a collagen VI VWA domain displays N and C termini at opposite sides of the protein
Authors: Becker, A.K. / Mikolajek, H. / Paulsson, M. / Wagener, R. / Werner, J.M.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha3(VI)


Theoretical massNumber of molelcules
Total (without water)21,6831
Polymers21,6831
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.070, 55.070, 106.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1434-

HOH

21A-1491-

HOH

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Components

#1: Protein Collagen alpha3(VI)


Mass: 21682.645 Da / Num. of mol.: 1 / Fragment: Collagen VI Alpha3 N5m, UNP residues 1022-1224 / Mutation: G1061R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57Bl6 / Gene: Col6a3 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q9Z0I9, UniProt: E9PWQ3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M sodium chloride, 0.1M phosphate/citrate, 20% PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.2→38.35 Å / Num. all: 53401 / Num. obs: 53401 / % possible obs: 99.7 % / Observed criterion σ(I): 19.3 / Redundancy: 6.6 % / Biso Wilson estimate: 11.09 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3739 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IGI

4igi


Resolution: 1.2→38.349 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 14.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1661 2707 5.08 %RANDOM
Rwork0.1388 ---
obs0.1401 53314 99.64 %-
all-53314 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.92 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 215 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081652
X-RAY DIFFRACTIONf_angle_d1.3192276
X-RAY DIFFRACTIONf_dihedral_angle_d12.118632
X-RAY DIFFRACTIONf_chiral_restr0.076268
X-RAY DIFFRACTIONf_plane_restr0.008313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21170.2231450.1888246495
1.2117-1.2350.26051280.17912658100
1.235-1.26020.17561270.16292617100
1.2602-1.28760.17991610.14862588100
1.2876-1.31750.21691290.14462645100
1.3175-1.35050.19671420.14342656100
1.3505-1.3870.191440.12882614100
1.387-1.42780.18581460.12382650100
1.4278-1.47390.16961400.12092628100
1.4739-1.52660.16871250.11322680100
1.5266-1.58770.13081470.1032641100
1.5877-1.660.12451600.10132653100
1.66-1.74750.14181470.10762647100
1.7475-1.8570.14821400.11412682100
1.857-2.00030.14361450.11872675100
2.0003-2.20160.14591530.11792709100
2.2016-2.52010.14571370.12912724100
2.5201-3.17490.19931390.15752761100
3.1749-38.36920.17161520.165291599

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