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- PDB-1zvg: Crystal Structure Of Mutant K8DP9S Of Scorpion alpha-Like Neuroto... -

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Basic information

Entry
Database: PDB / ID: 1zvg
TitleCrystal Structure Of Mutant K8DP9S Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch
ComponentsAlpha-like neurotoxin BmK-I
KeywordsTOXIN / scorpion alpha-like toxin / BMK M1 / mutant / mammal/insect selectivity
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-like toxin BmK M1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsYe, X. / Bosmans, F. / Li, C. / Zhang, Y. / Wang, D.C. / Tytgat, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural basis for the voltage-gated Na+ channel selectivity of the scorpion alpha-like toxin BmK M1
Authors: Ye, X. / Bosmans, F. / Li, C. / Zhang, Y. / Wang, D.C. / Tytgat, J.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-like neurotoxin BmK-I


Theoretical massNumber of molelcules
Total (without water)7,4121
Polymers7,4121
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.401, 44.338, 25.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

21A-157-

HOH

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Components

#1: Protein Alpha-like neurotoxin BmK-I / BmK I / BmKI / BmK1 / BmK-M1 / Bmk M1 / BmKM1


Mass: 7412.327 Da / Num. of mol.: 1 / Mutation: K10D, P11S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Gene: BMK M1 / Plasmid: PVT 102U-ALPHA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S-78 / References: UniProt: P45697
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5M sodium phosphates, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2000
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→23.7 Å / Num. all: 15517 / Num. obs: 15517 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 23.2
Reflection shellResolution: 1.2→1.28 Å / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.275 / % possible all: 58.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SN1.pdb

1sn1


Resolution: 1.2→23.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 279578.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1234 8 %RANDOM
Rwork0.158 ---
obs0.158 15517 89 %-
all-15517 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4454 Å2 / ksol: 0.333947 e/Å3
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.34 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.11 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.2→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 0 0 103 618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 1.2→1.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.187 119 7 %
Rwork0.209 1574 -
obs--59.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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