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- PDB-1r1g: Crystal Structure of the Scorpion Toxin BmBKTtx1 -

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Basic information

Entry
Database: PDB / ID: 1r1g
TitleCrystal Structure of the Scorpion Toxin BmBKTtx1
ComponentsNeurotoxin BmK37
KeywordsTOXIN / SIRAS from S atoms / scorpion toxin / BmBKTtx1 / reductive dimethylation
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 19.1
Function and homology information
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.72 Å
AuthorsSzyk, A. / Lu, W. / Xu, C. / Lubkowski, J.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Structure of the scorpion toxin BmBKTtx1 solved from single wavelength anomalous scattering of sulfur.
Authors: Szyk, A. / Lu, W. / Xu, C. / Lubkowski, J.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE ALL PRIMARY AMINO GROUPS (FIVE LYSINE RESIDUES AND THE N-TERMINUS) WERE DIMETHYLATED. ...SEQUENCE ALL PRIMARY AMINO GROUPS (FIVE LYSINE RESIDUES AND THE N-TERMINUS) WERE DIMETHYLATED. DENSITY WAS NOT SUFFICIENT TO MODEL THE METHYL GROUPS FOR THE N-TERMINUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotoxin BmK37
B: Neurotoxin BmK37


Theoretical massNumber of molelcules
Total (without water)7,0232
Polymers7,0232
Non-polymers00
Water1,946108
1
A: Neurotoxin BmK37


  • defined by author
  • 3.51 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3,5111
Polymers3,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neurotoxin BmK37


Theoretical massNumber of molelcules
Total (without water)3,5111
Polymers3,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.397, 39.695, 29.368
Angle α, β, γ (deg.)90.00, 94.13, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiologically active form of BmBKTx1 is a monomer.

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Components

#1: Protein/peptide Neurotoxin BmK37 / BmBKTtx1


Mass: 3511.301 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Sequence corresponds to that of naturally occuring toxin from scorpion Buthus martensi Karsch. Protein was synthesized using Boc chemistry. After folding all primary amino groups of BmBKTtx1 ...Details: Sequence corresponds to that of naturally occuring toxin from scorpion Buthus martensi Karsch. Protein was synthesized using Boc chemistry. After folding all primary amino groups of BmBKTtx1 (five lysine residues and the N-terminus) were dimethylated.
References: UniProt: P83407
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.77 Å3/Da / Density % sol: 30.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: sparse-matrix
Components of the solutions
*PLUS
Conc.: 100 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5478 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2003 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. all: 5064 / Num. obs: 5028 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 12.6 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 65.5
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 19 / Num. unique all: 491 / Rsym value: 0.089 / % possible all: 91.6
Reflection
*PLUS
Num. obs: 5064 / Num. measured all: 9834
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
HKL-2000data scaling
XPREPdata reduction
SHELXDphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.72→14.65 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 272 5.4 %RANDOM
Rwork0.166 ---
all-5028 --
obs-5028 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.9579 Å2 / ksol: 0.428433 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å2-1.33 Å2
2---1.59 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.72→14.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms480 0 0 108 588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it0.721.5
X-RAY DIFFRACTIONc_mcangle_it1.162
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 1.72→1.83 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.217 45 5.6 %
Rwork0.181 765 -
obs-804 91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 4756 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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