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- PDB-1kv0: Cis/trans Isomerization of Non-prolyl Peptide Bond Observed in Cr... -

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Basic information

Entry
Database: PDB / ID: 1kv0
TitleCis/trans Isomerization of Non-prolyl Peptide Bond Observed in Crystal Structure of an Scorpion Toxin
ComponentsAlpha-like toxin BmK-M7
KeywordsTOXIN / Non-prolyl cis peptide bond / Cis/trans isomerization / Dimeric structure / 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 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-M7
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGuan, R.J. / He, X.L. / Wang, M. / Xiang, Y. / Wang, D.C.
CitationJournal: 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.
History
DepositionJan 23, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-like toxin BmK-M7
B: Alpha-like toxin BmK-M7


Theoretical massNumber of molelcules
Total (without water)14,5052
Polymers14,5052
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.758, 32.758, 176.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-97-

HOH

21A-108-

HOH

31A-115-

HOH

41B-69-

HOH

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Components

#1: Protein Alpha-like toxin BmK-M7 / Bmk M7 / BmKM7


Mass: 7252.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Tissue: tail venom gland / References: UniProt: P59854
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, Tris-HCl, Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.65 Mammonium sulfate1reservoir
3100 mMTris-HCl1reservoirpH8.5
41 %(v/v)ethanol1reservoir

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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: Dec 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→29.3 Å / Num. obs: 19260 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.6 / % possible all: 74.6
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 57131 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 74.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.04refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SN1

1sn1


Resolution: 1.4→29.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.795 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16448 1898 9.9 %RANDOM
Rwork0.14194 ---
obs0.14416 17355 100 %-
all-19260 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 15.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 0 118 1159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211078
X-RAY DIFFRACTIONr_bond_other_d0.0030.02908
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9531476
X-RAY DIFFRACTIONr_angle_other_deg1.08632128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995135
X-RAY DIFFRACTIONr_chiral_restr0.1530.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021232
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02208
X-RAY DIFFRACTIONr_nbd_refined0.2290.2225
X-RAY DIFFRACTIONr_nbd_other0.2830.21004
X-RAY DIFFRACTIONr_nbtor_other0.0950.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8731.5678
X-RAY DIFFRACTIONr_mcangle_it3.06921088
X-RAY DIFFRACTIONr_scbond_it3.7053400
X-RAY DIFFRACTIONr_scangle_it5.594.5388
X-RAY DIFFRACTIONr_rigid_bond_restr1.90121078
X-RAY DIFFRACTIONr_sphericity_free9.3085118
X-RAY DIFFRACTIONr_sphericity_bonded3.41651041
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 110 10.2 %
Rwork0.153 1074 -
Refinement
*PLUS
Lowest resolution: 29.3 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.983
X-RAY DIFFRACTIONr_chiral_restr0.152

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