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- PDB-2k9c: Paramagnetic shifts in solid-state NMR of Proteins to elicit stru... -

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Basic information

Entry
Database: PDB / ID: 2k9c
TitleParamagnetic shifts in solid-state NMR of Proteins to elicit structural information
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / Matrix metalloproteinase / pseudocontact shift / paramagnetic NMR / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsBalayssac, S. / Bertini, I. / Bhaumik, A. / Lelli, M. / Luchinat, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Paramagnetic shifts in solid-state NMR of proteins to elicit structural information
Authors: Balayssac, S. / Bertini, I. / Bhaumik, A. / Lelli, M. / Luchinat, C.
History
DepositionOct 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _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 29, 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)16,8182
Polymers16,7591
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000target function
RepresentativeModel #1

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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: Catalytic domain of human MMP-12, 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: SOLUTION NMR / Details: Solid-State NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D PDSD
1212D CHHC
1323D NCACX
1423D NCOCX
1512D DARR
NMR detailsText: The structure was determined using a combination of distance restraints extracted from PDSD DARR, CHHC spectra, Talos calculated angles restraints and pseudocontact shift data

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Sample preparation

Details
Solution-IDContentsSolvent system
145mg/mL [U-100% 13C; U-100% 15N] ZnMMP12not applicable
245mg/mL [U-100% 13C; U-100% 15N] CoMMP12not applicable
315 + 30mg/mL [U-100% 13C; U-100% 15N] crystallized miture of 33% labelled ZnMMP-12 diluted with 67% of unlabeled CoMMP-12not applicable
415 + 30mg/mL [U-100% 13C; U-100% 15N] crystallized miture of 33% labelled CoMMP-12 diluted with 67% of unlabeled ZnMMP-12not applicable
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
45 mg/mLZnMMP12[U-100% 13C; U-100% 15N]1
45 mg/mLCoMMP12[U-100% 13C; U-100% 15N]2
15 mg/mLcrystallized miture of 33% labelled ZnMMP-12 diluted with 67% of unlabeled CoMMP-12[U-100% 13C; U-100% 15N]3
15 mg/mLcrystallized miture of 33% labelled CoMMP-12 diluted with 67% of unlabeled ZnMMP-12[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: low / pH: 8.0 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANAParamagneticCyanaGuntert, P.structure solution
CYANAParamagneticCyanaGuntert, P.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20 / Representative conformer: 16

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