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- PDB-2mun: Solution structure of mu-SLPTX3-Ssm6a -

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Basic information

Entry
Database: PDB / ID: 2mun
TitleSolution structure of mu-SLPTX3-Ssm6a
ComponentsMu-scoloptoxin-Ssm6a
KeywordsTOXIN / mu-SLPTX-Ssm6a / crustacean hyperglycemic hormone / ion channel inhibitor
Function / homologyDiphtheria Toxin Repressor; domain 2 - #50 / Diphtheria Toxin Repressor; domain 2 / sodium channel regulator activity / toxin activity / Orthogonal Bundle / extracellular region / Mainly Alpha / Mu-scoloptoxin(03)-Ssm2a
Function and homology information
Biological speciesScolopendra mutilans (arthropod)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsHighest molprobity percentile, model1
AuthorsUndheim, E.A.B. / King, G.F. / Mobli, M.
Citation
Journal: Structure / Year: 2015
Title: Weaponization of a Hormone: Convergent Recruitment of Hyperglycemic Hormone into the Venom of Arthropod Predators.
Authors: Undheim, E.A. / Grimm, L.L. / Low, C.F. / Morgenstern, D. / Herzig, V. / Zobel-Thropp, P. / Pineda, S.S. / Habib, R. / Dziemborowicz, S. / Fry, B.G. / Nicholson, G.M. / Binford, G.J. / Mobli, M. / King, G.F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Discovery of a selective NaV1.7 inhibitor from centipede venom with analgesic efficacy exceeding morphine in rodent pain models.
Authors: Yang, S. / Xiao, Y. / Kang, D. / Liu, J. / Li, Y. / Undheim, E.A. / Klint, J.K. / Rong, M. / Lai, R. / King, G.F.
History
DepositionSep 13, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu-scoloptoxin-Ssm6a


Theoretical massNumber of molelcules
Total (without water)5,3331
Polymers5,3331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 30target function
RepresentativeModel #1highest molprobity percentile

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Components

#1: Protein/peptide Mu-scoloptoxin-Ssm6a / Mu-SLPTX-Ssm6a


Mass: 5333.003 Da / Num. of mol.: 1 / Fragment: UNP residues 66-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scolopendra mutilans (arthropod) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0DL36
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D HBHA(CO)NH
1323D CBCA(CO)NH
1423D HNCO
1523D 1H-15N NOESY
1623D 1H-13C NOESY aliphatic
1723D 1H-13C NOESY aromatic
1823D 1H-15N TOCSY
1922D 1H-13C HSQC
11012D 1H-1H TOCSY
11112D 1H-1H NOESY
NMR detailsText: Mixing time 180 ms for all NOESY experiments. 3D backbone experiments acquired using NUS and processed using the maximum entropy method.

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM [U-13C; U-15N] mu-SLPTX3-Ssm6a, 20 mM ammonium acetate, 5 % [U-99% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
2300 uM mu-SLPTX3-Ssm6a, 20 mM ammonium acetate, 5 % [U-99% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMmu-SLPTX3-Ssm6a-1[U-13C; U-15N]1
20 mMammonium acetate-21
5 %D2O-3[U-99% 2H]1
300 uMmu-SLPTX3-Ssm6a-42
20 mMammonium acetate-52
5 %D2O-6[U-99% 2H]2
Sample conditionspH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
AnalysisCCPNpeak picking
AnalysisCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxchemical shift calculation
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
Rowland_NMR_ToolkitUniversity of Connecticutprocessing
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Using automated NOE assignment routine within CYANA.
NMR constraintsNOE constraints total: 1576 / NOE intraresidue total count: 788 / NOE long range total count: 128 / NOE medium range total count: 211 / NOE sequential total count: 449 / Disulfide bond constraints total count: 18 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41
NMR representativeSelection criteria: highest molprobity percentile
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 25

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