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- PDB-2krj: High-Resolution Solid-State NMR Structure of a 17.6 kDa Protein -

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Entry
Database: PDB / ID: 2krj
TitleHigh-Resolution Solid-State NMR Structure of a 17.6 kDa Protein
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / 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
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)
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBertini, I. / Bhaumik, A. / De Pa pe, G. / Griffin, R.G. / Lelli, M. / Lewandowski, J.R. / Luchinat, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: High-resolution solid-state NMR structure of a 17.6 kDa protein.
Authors: Bertini, I. / Bhaumik, A. / De Paepe, G. / Griffin, R.G. / Lelli, M. / Lewandowski, J.R. / Luchinat, C.
History
DepositionDec 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_nmr_spectrometer ...pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8182
Polymers16,7591
Non-polymers591
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 / 2000target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 16758.594 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 112-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PDSD
121CHHC
131DARR
141PAIN
151PAR
NMR detailsText: The structure was determined using a combination of Distance restrains collected from different experiments data, TALOS angle restraints and Pseudo contact shifts data.

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Sample preparation

DetailsContents: 45 mg/mL [U-100% 13C; U-100% 15N] protein, PEG / Solvent system: PEG
SampleConc.: 45 mg/mL / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 8 / Pressure: ambient / Temperature: 270 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR softwareName: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20 / Representative conformer: 1

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