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- PDB-2k72: Solution NMR structure of toxin-like potassium channel blocking d... -

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Basic information

Entry
Database: PDB / ID: 2k72
TitleSolution NMR structure of toxin-like potassium channel blocking domain in MMP23
ComponentsMatrix metalloproteinase-23
KeywordsHYDROLASE / toxin / metalloprotease / MMP23 / potassium channel / Cleavage on pair of basic residues / Glycoprotein / Immunoglobulin domain / Membrane / Metal-binding / Signal-anchor / Transmembrane / Zinc / Zymogen
Function / homology
Function and homology information


: / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / membrane => GO:0016020 / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Matrix metalloproteinase-23 / ShK toxin domain / ShK domain-like / ShKT domain / ShKT domain profile. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase ...Matrix metalloproteinase-23 / ShK toxin domain / ShK domain-like / ShKT domain / ShKT domain profile. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Matrix metalloproteinase-23
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsKhoo, K.K. / Feng, Z. / Norton, R.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Potassium channel modulation by a toxin domain in matrix metalloprotease 23.
Authors: Rangaraju, S. / Khoo, K.K. / Feng, Z.P. / Crossley, G. / Nugent, D. / Khaytin, I. / Chi, V. / Pham, C. / Calabresi, P. / Pennington, M.W. / Norton, R.S. / Chandy, K.G.
History
DepositionJul 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix metalloproteinase-23


Theoretical massNumber of molelcules
Total (without water)4,4421
Polymers4,4421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Matrix metalloproteinase-23 / MMP-23 / Matrix metallopeptidase 23 / Metalloprotease in the female reproductive tract / MIFR


Mass: 4442.336 Da / Num. of mol.: 1 / Fragment: UNP residues 254-290 / Source method: obtained synthetically
Details: Synthetic peptide MMP23-BgK with the sequence based on the residues 254-290 of Rattus norvegicus matrix metalloproteinase-23, UniProt entry O88272, MMP23_RAT
References: UniProt: O88272, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
2312D DQF-COSY
2412D 1H-13C HSQC
2512D 1H-15N HSQC
1622D 1H-1H TOCSY
1722D 1H-1H NOESY
2812D 1H-1H TOCSY
2912D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.25 mM MMP23-BgK, 94% H2O/6% D2O94% H2O/6% D2O
22.2 mM MMP23-BgK, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.25 mMMMP23-BgK1
2.2 mMMMP23-BgK2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.00 ambient 278 K
25.00 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
XEASY1.3.13Bartels et al.processing
XEASY1.3.13Bartels et al.collection
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 2 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å

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