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- PDB-1kth: The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom -

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Basic information

Entry
Database: PDB / ID: 1kth
TitleThe Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom
ComponentsCollagen alpha 3(VI) chain
KeywordsSTRUCTURAL PROTEIN / ANISOTROPIC REFINEMENT / KUNITZ 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 / FOURIER SYNTHESIS / Resolution: 0.95 Å
AuthorsArnoux, B. / Ducruix, A. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A).
Authors: Arnoux, B. / Ducruix, A. / Prange, T.
#1: Journal: 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.
#2: Journal: 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 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 16, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha 3(VI) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8293
Polymers6,6401
Non-polymers1902
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.270, 37.800, 28.510
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Collagen alpha 3(VI) chain


Mass: 6639.508 Da / Num. of mol.: 1 / Fragment: Kunitz-type Domain C5, C-Terminus
Source method: isolated from a genetically manipulated source
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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.55 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: phosphate buffer, sodium sulfate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 K / 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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1998
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→8 Å / Num. all: 28107 / Num. obs: 22448 / % possible obs: 90.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 0.95→0.97 Å / Rmerge(I) obs: 0.051 / Num. unique all: 1598 / % possible all: 85.2
Reflection
*PLUS
Highest resolution: 0.95 Å / Num. obs: 33572 / % possible obs: 95.2 % / Num. measured all: 179075 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2KNT

2knt


Resolution: 0.95→5 Å / Num. parameters: 5097 / Num. restraintsaints: 6007 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1667 1460 5.2 %RANDOM
Rwork0.135 ---
all0.1391 28107 --
obs0.1355 22448 88.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 551.81
Refinement stepCycle: LAST / Resolution: 0.95→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 10 86 566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0326
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.083
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 0 / Num. reflection Rfree: 1147 / % reflection Rfree: 6 % / Rfactor all: 0.132 / Rfactor obs: 0.121 / Rfactor Rfree: 0.162 / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.041

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