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- PDB-2jxy: Solution structure of the hemopexin-like domain of MMP12 -

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Basic information

Entry
Database: PDB / ID: 2jxy
TitleSolution structure of the hemopexin-like domain of MMP12
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / b-sheet hydrophobic core / Calcium / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain ...4 Propeller / Hemopexin / Hemopexin-like domain / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Mainly Beta
Similarity search - Domain/homology
Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBertini, I. / Calderone, V. / Fragai, M. / Jaiswal, R. / Luchinat, C. / Melikian, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12
Authors: Bertini, I. / Calderone, V. / Fragai, M. / Jaiswal, R. / Luchinat, C. / Melikian, M. / Mylonas, E. / Svergun, D.I.
History
DepositionDec 1, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2412
Polymers23,2001
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1600lowest target function
RepresentativeModel #1rmsd closest to mean

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Components

#1: Protein Macrophage metalloelastase / HME / Matrix metalloproteinase-12 / MMP-12 / Macrophage elastase / ME


Mass: 23200.453 Da / Num. of mol.: 1 / Fragment: Hemopexin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: Acquired and processed using topspin software.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-100% 13C; U-100% 15N] HPX_DOMAIN, 90% H2O, 10% D2O90% H2O/10% D2O
20.7mM [U-100% 15N] HPX_DOMAIN, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHPX_DOMAIN[U-100% 13C; U-100% 15N]1
0.7 mMHPX_DOMAIN[U-100% 15N]2
Sample conditionsIonic strength: 300 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX5002

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Processing

NMR softwareName: DYANA / Developer: Guntert, Braun and Wuthrich / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: 20000 steps
NMR constraintsNOE constraints total: 3890 / Disulfide bond constraints total count: 1 / Hydrogen bond constraints total count: 72 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 95 / Protein psi angle constraints total count: 94
NMR representativeSelection criteria: rmsd closest to mean
NMR ensembleConformer selection criteria: lowest target function / Conformers calculated total number: 1600 / Conformers submitted total number: 20

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