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- PDB-1t7e: Crystal structure of mutant Pro9Ser of scorpion alpha-like neurot... -

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Basic information

Entry
Database: PDB / ID: 1t7e
TitleCrystal structure of mutant Pro9Ser of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch
ComponentsAlpha-like neurotoxin BmK-I
KeywordsTOXIN / BmK M1 mutant / Scorpion toxin / Buthus martensii Karsch
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
PHOSPHATE ION / Alpha-like toxin BmK M1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 9, 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type

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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)7,7114
Polymers7,4261
Non-polymers2853
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.907, 46.907, 53.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 7426.419 Da / Num. of mol.: 1 / Mutation: P9S
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium phosphate, PEG400, pH 4.6, 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: 1.4→30 Å / Num. all: 13889 / Num. obs: 13889 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 7.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / Num. unique all: 1988 / Rsym value: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SN1

1sn1


Resolution: 1.4→19 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.464 / SU ML: 0.059 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21589 1405 10.2 %RANDOM
Rwork0.1924 ---
all0.19494 13889 --
obs0.19494 13889 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 15 51 586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021549
X-RAY DIFFRACTIONr_bond_other_d0.0010.02435
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.955747
X-RAY DIFFRACTIONr_angle_other_deg0.74831025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.658365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4251594
X-RAY DIFFRACTIONr_chiral_restr0.0970.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02609
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02108
X-RAY DIFFRACTIONr_nbd_refined0.1990.3112
X-RAY DIFFRACTIONr_nbd_other0.2060.3405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.548
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.50.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.313
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.58
X-RAY DIFFRACTIONr_mcbond_it1.1511.5327
X-RAY DIFFRACTIONr_mcangle_it2.1412523
X-RAY DIFFRACTIONr_scbond_it2.7943222
X-RAY DIFFRACTIONr_scangle_it4.1064.5224
LS refinement shellHighest resolution: 1.4 Å / Num. reflection Rwork: 1178 / Total num. of bins used: 15

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