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- PDB-2knt: THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5 -

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Basic information

Entry
Database: PDB / ID: 2knt
TitleTHE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5
ComponentsCOLLAGEN
KeywordsKUNITZ INHIBITOR / EXTRACELLULAR MATRIX / CONNECTIVE TISSUE
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
PHOSPHATE ION / Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMerigeau, K. / Arnoux, B. / Ducruix, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: 1.2 A refinement of the Kunitz-type domain from the alpha3 chain of human type VI collagen.
Authors: Merigeau, K. / Arnoux, B. / Perahia, D. / Norris, K. / Norris, F. / Ducruix, A.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7342
Polymers6,6401
Non-polymers951
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.690, 38.040, 28.640
Angle α, β, γ (deg.)90.00, 109.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COLLAGEN


Mass: 6639.508 Da / Num. of mol.: 1 / Fragment: DOMAIN C5, C-TERMINUS OF TYPE VI COLLAGEN
Source method: isolated from a genetically manipulated source
Details: KUNITZ-TYPE / Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): MT-663 / References: UniProt: P12111
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 39 %
Crystal growpH: 3.3
Details: 0.2M LI2SO4, 0.1M CITRIC ACID, 0.074M NA2HPO4, 1.6M (NH4)2SO4, 10MG/ML, PH3.3
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 3 / Method: vapor diffusion, sitting drop / Details: Arnoux, B., (1995) J. Mol. Biol., 246, 609.
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

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 14, 1995
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.18→20.4 Å / Num. obs: 16657 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 46.5
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.09 / Rsym value: 0.75 / % possible all: 52.5
Reflection
*PLUS
Num. measured all: 84000
Reflection shell
*PLUS
% possible obs: 61 %

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Processing

Software
NameClassification
MOSFLMdata reduction
Agrovatadata reduction
AMoREphasing
SHELXL-93refinement
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAP

1aap


Resolution: 1.2→7 Å / Num. restraintsaints: 5876 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1600 10 %EVERY 10TH REFLECTION
all0.1489 16307 --
obs0.1455 -96 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 630 / Occupancy sum non hydrogen: 476
Refinement stepCycle: LAST / Resolution: 1.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 5 51 532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.016
X-RAY DIFFRACTIONs_zero_chiral_vol0.148
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.13
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.108
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 10762
Solvent computation
*PLUS
Displacement parameters
*PLUS

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