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- PDB-1t7a: Crystal structure of mutant Lys8Asp of scorpion alpha-like neurot... -

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Basic information

Entry
Database: PDB / ID: 1t7a
TitleCrystal structure of mutant Lys8Asp of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch
ComponentsAlpha-like neurotoxin BmK-I
KeywordsTOXIN / Intramolecular Switch / Cis/Trans Isomerization / Non-Proline peptide Bond / Scorpion Toxin
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: 1.5 Å
AuthorsXiang, Y. / Guan, R.J. / He, X.L. / Wang, C.G. / Wang, M. / Zhang, Y. / Sundberg, E.J. / Wang, D.C.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural Mechanism Governing Cis and Trans Isomeric States and an Intramolecular Switch for Cis/Trans Isomerization of a Non-proline Peptide Bond Observed in Crystal Structures of Scorpion Toxins
Authors: Guan, R.J. / Xiang, Y. / He, X.L. / Wang, C.G. / Wang, M. / Zhang, Y. / Sundberg, E.J. / Wang, D.C.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of two alpha-like scorpion toxins: non-proline cis peptide bonds and implications for new binding site selectivity on the sodium channel
Authors: He, X.L. / Li, H.M. / Zeng, Z.H. / Liu, X.Q. / Wang, M. / Wang, D.C.
#2: Journal: Protein Expr.Purif. / Year: 1999
Title: Expression and purification of the BmK M1 neurotoxin from the scorpion Buthus martensii Karsch
Authors: Shao, F. / Xiong, Y.M. / Zhu, R.H. / Ling, M.H. / Chi, C.W. / Wang, D.C.
#3: Journal: Toxicon / Year: 1997
Title: The CDNA and genomic DNA sequences of a mammalian neurotoxin from the scorpion Buthus martensii Karsch
Authors: Xiong, Y.M. / Ling, M.H. / Wang, D.C. / Chi, C.W.
History
DepositionMay 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: 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 1.5Nov 13, 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)7,4221
Polymers7,4221
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.452, 44.343, 25.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 7422.364 Da / Num. of mol.: 1 / Mutation: K8D
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.: 84 / 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: sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 283 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: 1.5→30 Å / Num. all: 8946 / Num. obs: 8946 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 28.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 8.7 / Num. unique all: 814 / Rsym value: 0.175 / % possible all: 93.3

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Processing

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

1sn1


Resolution: 1.5→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 247438.47 / 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
Rfree0.183 617 7 %RANDOM
Rwork0.165 ---
obs0.165 8946 96.7 %-
all-8946 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0976 Å2 / ksol: 0.335499 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--2.09 Å20 Å2
3----0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 84 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellHighest resolution: 1.5 Å / Num. reflection Rwork: 1341 / Total num. of bins used: 6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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