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- PDB-1zyw: Crystal Structure Of Mutant K8DP9SR58KP60G Of Scorpion alpha-Like... -

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Entry
Database: PDB / ID: 1zyw
TitleCrystal Structure Of Mutant K8DP9SR58KP60G 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
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / 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 ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / 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
ACETATE ION / Alpha-like toxin BmK M1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-like neurotoxin BmK-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5954
Polymers7,3441
Non-polymers2513
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.862, 43.538, 25.426
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-2079-

HOH

21A-2080-

HOH

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Components

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


Mass: 7344.250 Da / Num. of mol.: 1 / Mutation: K10D, P11S, R60K, P62G
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 6.5
Details: 30% (w/v) PEG8000, 0.1M sodium cacodylate pH 6.5, 0.2M ammonium sulfate, 0.02M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→22.4 Å / Num. all: 13231 / Num. obs: 13231 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.2
Reflection shellResolution: 1.3→1.38 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.152 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SN1.pdb

1sn1


Resolution: 1.3→22.35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 961833.57 / 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
Rfree0.171 1268 9.6 %RANDOM
Rwork0.143 ---
obs0.143 13231 99 %-
all-13231 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1665 Å2 / ksol: 0.354135 e/Å3
Displacement parametersBiso mean: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--1.37 Å20 Å2
3----0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.1 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.02 Å
Refinement stepCycle: LAST / Resolution: 1.3→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 0 14 81 605
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.178 220 10.2 %
Rwork0.145 1935 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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