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- PDB-1ks0: The First Fibronectin Type II Module from Human Matrix Metallopro... -

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Basic information

Entry
Database: PDB / ID: 1ks0
TitleThe First Fibronectin Type II Module from Human Matrix Metalloproteinase 2
ComponentsMatrix Metalloproteinase 2Gelatinase A
KeywordsHYDROLASE / beta sheet / alpha helix / 3/1 helix
Function / homology
Function and homology information


gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / protein metabolic process / cellular response to fluid shear stress / negative regulation of cell adhesion / face morphogenesis / negative regulation of vasoconstriction / macrophage chemotaxis / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / fibronectin binding / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / response to hyperoxia / ephrin receptor signaling pathway / cellular response to interleukin-1 / response to electrical stimulus / response to mechanical stimulus / response to retinoic acid / ovarian follicle development / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / sarcomere / extracellular matrix organization / response to activity / response to nicotine / cellular response to estradiol stimulus / cellular response to amino acid stimulus / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / heart development / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / Extra-nuclear estrogen signaling / response to hypoxia / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / plasma membrane
Similarity search - Function
Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. ...Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / Ribbon / Mainly Beta
Similarity search - Domain/homology
72 kDa type IV collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsGehrmann, M. / Briknarova, K. / Banyai, L. / Patthy, L. / Llinas, M.
CitationJournal: Biol.Chem. / Year: 2002
Title: The col-1 module of human matrix metalloproteinase-2 (MMP-2): structural/functional relatedness between gelatin-binding fibronectin type II modules and lysine-binding kringle domains.
Authors: Gehrmann, M. / Briknarova, K. / Banyai, L. / Patthy, L. / Llinas, M.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix Metalloproteinase 2


Theoretical massNumber of molelcules
Total (without water)7,2771
Polymers7,2771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 50all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Matrix Metalloproteinase 2 / Gelatinase A / 72 Kda Type IV Collagenase / MMP-2


Mass: 7277.104 Da / Num. of mol.: 1 / Fragment: First Fibronectin Type II Module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08253, gelatinase A

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
233HNHA
243HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM col-1; 90% H2O, 10% d6-acetone90% H2O, 10% d6-acetone
20.5mM col-1; 90% D2O, 10% d6-acetone90% D2O, 10% d6-acetone
30.7mM col-1 15N; 90% H2O, 10% d6-acetone90% H2O, 10% d6-acetone
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 7.3 ambient 298 K
20 6.0 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
Felix98MSIprocessing
Felix98MSIdata analysis
X-PLOR3.851Brungerrefinement
X-PLOR3.851Brungerstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 50

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