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- PDB-2poj: NMR Solution Structure of the Inhibitor-Free State of Macrophage ... -

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Basic information

Entry
Database: PDB / ID: 2poj
TitleNMR Solution Structure of the Inhibitor-Free State of Macrophage Metalloelastase (MMP-12)
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / INHIBITOR-FREE SOLUTION STRUCTURE / MATRIX METALOPROTEINASE / MACROPHAGE METALLOELASTASE / MMP-12
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
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 ...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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES.
AuthorsBhaskaran, R. / Van Doren, S.R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure of Inhibitor-Free Human Metalloelastase (MMP-12) Indicates an Internal Conformational Adjustment.
Authors: Bhaskaran, R. / Palmier, M.O. / Bagegni, N.A. / Liang, X. / Van Doren, S.R.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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_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_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4286
Polymers18,1771
Non-polymers2515
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 18177.373 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: E219A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Plasmid: pET 21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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
1113D 15N-separated NOESY
2223D 13C-separated NOESY
232HNCA-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY AND AUTOMATED ANALYSIS OF 3D STRUCTURE. THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION NMR DATA. PROTEIN DATA ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY AND AUTOMATED ANALYSIS OF 3D STRUCTURE. THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE RECORDS ARE MEANINGLESS.

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Sample preparation

Details
Solution-IDContentsSolvent system
11. Uniform labeling with 15N: U-15N 20mM Imidazole; 10mM CaCl2; 20 uM ZnCl2; 90% H2O, 10% D2O90% H2O/10% D2O
22. Uniform labeling with 13C, 15N: U-15N,13C 20mM Imidazole ; 10mM CaCl2; 20 uM ZnCl2; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 20mM Imidazole,10mM CaCl2 and 20uM ZnCl2 / pH: 6.6 / Temperature: 299 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associatescollection
NMRPipe2.6Delaglio, Fprocessing
Sparky3Goddard, T. Ddata analysis
CYANA2.1Guentert, Prefinement
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, AUTOMATED ANALYSIS OF NOESY DATA, 3D STRUCTURES.
Software ordinal: 1
Details: the structures are based on a total of 2813 NOE-derived distance constraints and 220 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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