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- PDB-1cxw: THE SECOND TYPE II MODULE FROM HUMAN MATRIX METALLOPROTEINASE 2 -

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Basic information

Entry
Database: PDB / ID: 1cxw
TitleTHE SECOND TYPE II MODULE FROM HUMAN MATRIX METALLOPROTEINASE 2
ComponentsHUMAN MATRIX METALLOPROTEINASE 2
KeywordsHYDROLASE / BETA SHEET / ALPHA HELIX
Function / homology
Function and homology information


gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / 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 / Activation of Matrix Metalloproteinases / endodermal cell differentiation / macrophage chemotaxis / response to amyloid-beta / fibronectin binding / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / response to hyperoxia / cellular response to interleukin-1 / response to electrical stimulus / response to mechanical stimulus / response to retinoic acid / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / embryo implantation / Degradation of the extracellular matrix / sarcomere / extracellular matrix organization / response to activity / cellular response to estradiol stimulus / cellular response to amino acid stimulus / response to nicotine / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / 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 / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsBriknarova, K. / Grishaev, A. / Banyai, L. / Tordai, H. / Patthy, L. / Llinas, M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The second type II module from human matrix metalloproteinase 2: structure, function and dynamics.
Authors: Briknarova, K. / Grishaev, A. / Banyai, L. / Tordai, H. / Patthy, L. / Llinas, M.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN MATRIX METALLOPROTEINASE 2


Theoretical massNumber of molelcules
Total (without water)6,7731
Polymers6,7731
Non-polymers00
Water00
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 #1fewest violations,lowest energy

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Components

#1: Protein HUMAN MATRIX METALLOPROTEINASE 2 / COL-2


Mass: 6773.364 Da / Num. of mol.: 1 / Fragment: THE SECOND TYPE II MODULE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PMED23 / 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
2222D NOESY
232E-COSY
144HNHA
154HNHB

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Sample preparation

Details
Solution-IDContents
11.3MM COL-2 NA; 90% H2O, 10% D2O
21.3MM COL-2 NA; D2O
31MM COL-2 U-15N; 90% H2O, 10% D2O
44MM COL-2 U-15N; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 5.2 1 atm298 K
20 5.1 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2BRUKER, GERMANYstructure solution
Felix95MOLECULAR SIMULATIONS, INC., SAN DIEGO, CAstructure solution
X-PLOR3.851BRUNGERstructure solution
QUANTA96MOLECULAR SIMULATIONS, INC., SAN DIEGO, CArefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 50

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