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- PDB-7px1: Conotoxin from Conus mucronatus -

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Basic information

Entry
Database: PDB / ID: 7px1
TitleConotoxin from Conus mucronatus
ComponentsConus mucronatus
KeywordsTOXIN / Conotoxin / Conus mucronatus
Function / homology: / IODIDE ION
Function and homology information
Biological speciesConus mucronatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsMueller, E. / Hackney, C.M. / Ellgaard, L. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Plos Biol. / Year: 2023
Title: A previously unrecognized superfamily of macro-conotoxins includes an inhibitor of the sensory neuron calcium channel Cav2.3.
Authors: Hackney, C.M. / Florez Salcedo, P. / Mueller, E. / Koch, T.L. / Kjelgaard, L.D. / Watkins, M. / Zachariassen, L. / Tuelund, P.S. / McArthur, J.R. / Adams, D.J. / Kristensen, A.S. / Olivera, ...Authors: Hackney, C.M. / Florez Salcedo, P. / Mueller, E. / Koch, T.L. / Kjelgaard, L.D. / Watkins, M. / Zachariassen, L. / Tuelund, P.S. / McArthur, J.R. / Adams, D.J. / Kristensen, A.S. / Olivera, B. / Finol-Urdaneta, R.K. / Safavi-Hemami, H. / Morth, J.P. / Ellgaard, L.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conus mucronatus
B: Conus mucronatus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,98415
Polymers20,4072
Non-polymers1,57713
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-49 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.300, 109.360, 34.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Conus mucronatus


Mass: 10203.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus mucronatus (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M NaOAc, 0.1M CdCl hemi(pentahydrate), pH 4.6, 30% w/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.33→36.62 Å / Num. obs: 8423 / % possible obs: 99.67 % / Redundancy: 12.3 % / Biso Wilson estimate: 47.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2101 / Rpim(I) all: 0.06378 / Rrim(I) all: 0.2199 / Net I/σ(I): 7.62
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 12.8 % / Num. unique obs: 811 / CC1/2: 0.607 / CC star: 0.869 / Rpim(I) all: 0.3774 / % possible all: 99.88

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Processing

Software
NameVersionClassification
Coot1.19.2_4158model building
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→44.94 Å / SU ML: 0.4136 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 37.6142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 812 5.31 %
Rwork0.2605 14472 -
obs0.2629 15284 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.65 Å2
Refinement stepCycle: LAST / Resolution: 2.33→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 13 27 1386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261374
X-RAY DIFFRACTIONf_angle_d0.49771860
X-RAY DIFFRACTIONf_chiral_restr0.0305214
X-RAY DIFFRACTIONf_plane_restr0.0024232
X-RAY DIFFRACTIONf_dihedral_angle_d4.9486186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.480.44041430.35852415X-RAY DIFFRACTION99.77
2.48-2.670.37871300.31682417X-RAY DIFFRACTION99.73
2.67-2.940.34281510.36062378X-RAY DIFFRACTION99.49
2.94-3.360.37121320.27942429X-RAY DIFFRACTION99.69
3.36-4.230.29131280.23752416X-RAY DIFFRACTION99.76
4.23-44.940.23991280.21812417X-RAY DIFFRACTION99.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.510034580270.5917197805261.527032797264.835793924824.843614236735.2087575029-0.09838099989080.286167818029-0.990887339996-1.594689094021.003573428-0.65651603585-0.2992110883871.06408476702-0.9031495712850.7010182342740.09314567092640.08942384549440.801400555846-0.06716742381970.728528112054.158443448437.5696770889-9.96991395524
24.114041357750.171331811121-1.166085541672.880093707180.3842565280271.99434255306-0.0204707817616-0.118003027379-0.1631810171080.35596333591-0.1395174788330.4525435945570.0496537803018-0.006480631492050.1273919539570.545127064722-0.0566930229010.0358751118970.50629013872-0.02592637203790.6410154601713.6576318796432.75238937723.71241569489
33.76563981770.5277525621691.664109068844.44897293975-0.9863471984342.40220243576-0.363003811773-0.1728670074230.2621346957230.1040558821320.04476841762190.6915369623870.1047421953180.04978951879760.07758587756620.4648061339930.006790368206940.0245585713360.461079221082-0.02524343156360.5606238721946.2527488523244.52302845881.75553685597
47.70438619272-1.980423437380.3515512609699.597267424263.070479088286.897603860480.15571629083-0.507052904664-0.3582174753410.408866807754-0.6261464973011.60450317461-1.13491386374-0.09340018680530.5389770418620.711940303546-0.01698887516420.02935533647690.611867551287-0.02787526241830.65390163011-3.6040784411647.50829162062.00457692894
51.008989973090.03496507880420.01395746033431.367305731173.314774990498.063911287410.08063032942-0.168579663960.1266488023760.964215186285-0.06415351568170.167403403891-0.297983674224-1.04871614559-0.2357326190980.8029370590710.070409023359-0.04976024135860.6777805819330.03782371820770.6507485920658.3697868321551.7339062184-4.22512214636
63.97348892076-1.23841649923-1.11003324944.291420438261.124976469053.877392562850.07202738169160.2028332074320.08286240260311.455098602890.6922835145740.4560703789351.30047530675-1.40815208282-0.7565530986320.757633437077-0.1365804046630.0002142287274250.5874352685290.1597453442980.44278192534821.113810609235.774048408411.3759616266
73.20438553579-0.558370766170.5351611131412.77411403088-0.7167377118092.457713122830.118312141260.0776151635037-0.218586749124-0.343467382129-0.09486174969580.0168850889508-0.026351354690.202064326133-0.1078446522910.549797663545-0.001532357635930.03175419203850.525026771423-0.02280273553210.54018900944521.404755370433.5713163949-2.27430861004
81.324900938711.16294790488-0.7341621103551.38286130249-0.6535039489821.52551008692-0.124558254160.3121970896870.023212849288-0.3659564851260.0793546568821-0.1367120937170.253798303283-0.007465019495460.04291083824220.5443743361110.03260379686880.08750718129010.4989001353110.00171959701510.56345039767919.261670543645.42479735230.564133951531
94.741669125230.76967845430.1031801297466.017976298680.08317098599678.081584566820.2033744693190.5820367118510.0588004512673-0.101317801727-0.0711751649124-1.21229806084-1.796318300210.398957587214-0.2481020070280.669937435370.007817759589270.0285468078090.533779412564-0.031881939710.57678958315628.667589914447.63769620541.55889606982
103.63487944403-1.765668645350.6178513031855.16590447658-2.720216862754.100996475140.465617456461-0.1078657520150.4018705522610.138013667844-0.7578642152111.620367050490.0984817291593-0.2828053222480.5504273219150.750147023796-0.0102101336321-0.01840071715910.520030672036-0.1316047453510.82725432124616.725718086851.03775575788.36659430536
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 11 )AA6 - 111 - 6
22chain 'A' and (resid 12 through 47 )AA12 - 477 - 42
33chain 'A' and (resid 48 through 65 )AA48 - 6543 - 60
44chain 'A' and (resid 66 through 78 )AA66 - 7861 - 73
55chain 'A' and (resid 79 through 89 )AA79 - 8974 - 84
66chain 'B' and (resid 6 through 11 )BB6 - 111 - 6
77chain 'B' and (resid 12 through 48 )BB12 - 487 - 43
88chain 'B' and (resid 49 through 65 )BB49 - 6544 - 60
99chain 'B' and (resid 66 through 78 )BB66 - 7861 - 73
1010chain 'B' and (resid 79 through 89 )BB79 - 8974 - 84

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