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- PDB-1knt: THE 1.6 ANGSTROMS STRUCTURE OF THE KUNITZ-TYPE DOMAIN FROM THE AL... -

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Basic information

Entry
Database: PDB / ID: 1knt
TitleTHE 1.6 ANGSTROMS STRUCTURE OF THE KUNITZ-TYPE DOMAIN FROM THE ALPHA3 CHAIN OF THE HUMAN TYPE VI COLLAGEN
ComponentsCOLLAGEN TYPE VI
KeywordsCOLLAGEN TYPE VI FRAGMENT
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 / Assembly of collagen fibrils and other multimeric structures / muscle organ development / 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 / Assembly of collagen fibrils and other multimeric structures / muscle organ development / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / response to glucose / response to UV / extracellular matrix / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / extracellular vesicle / : / neuron apoptotic process / cell adhesion / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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. ...Collagen alpha-3(VI) chain, vWA domain / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Few Secondary Structures / Irregular / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsArnoux, B. / Merigeau, K. / Saludjian, P. / Norris, F. / Norris, K. / Bjorn, S. / Olsen, O. / Petersen, L. / Ducruix, A.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: The 1.6 A structure of Kunitz-type domain from the alpha 3 chain of human type VI collagen.
Authors: Arnoux, B. / Merigeau, K. / Saludjian, P. / Norris, F. / Norris, K. / Bjorn, S. / Olsen, O. / Petersen, L. / Ducruix, A.
History
DepositionAug 18, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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

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Assembly

Deposited unit
A: COLLAGEN TYPE VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7362
Polymers6,6401
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.700, 38.200, 28.800
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COLLAGEN TYPE VI


Mass: 6639.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12111
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE TERTIARY STRUCTURE OF THE C5 FRAGMENT IS VERY CLOSE TO ALL OTHER MEMBERS OF THE KUNITZ FAMILY.
Has protein modificationY
Nonpolymer detailsONE SULFATE ION LINKS MOLECULE OF SYMMETRY 1 WITH MOLECULE OF SYMMETRY 1 - X, Y, Z.
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM HUMAN COLLAGEN ALPHA3 (VI) CHAIN MRNA AND ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM HUMAN COLLAGEN ALPHA3 (VI) CHAIN MRNA AND CONFIRMED BY CHU ET AL., EMBO JOURNAL, VOL. 9, 385, (1990).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.2 M1reservoirLi2SO4
30.1 Mcitric acid1reservoir
40.074 M1reservoirNa2HPO4
51.45 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 8388 / % possible obs: 92 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 18393 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.62 Å / % possible obs: 83 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 6276 82 %
Displacement parametersBiso mean: 15.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 5 43 488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 6276 / Rfactor all: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.45

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