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- PDB-4kyp: Beta-Scorpion Toxin folded in the periplasm of E.coli -

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Basic information

Entry
Database: PDB / ID: 4kyp
TitleBeta-Scorpion Toxin folded in the periplasm of E.coli
ComponentsBeta-insect excitatory toxin Bj-xtrIT
KeywordsTOXIN / Alpha-Beta / Venom / Voltage Gated Na-Channels
Function / homology
Function and homology information


sodium channel inhibitor activity / toxin activity / extracellular region
Similarity search - Function
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 / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Beta-insect excitatory toxin Bj-xtrIT
Similarity search - Component
Biological speciesHottentotta judaicus (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsO'Reilly, A.O. / Cole, A.R. / Lopes, J.L. / Lampert, A. / Wallace, B.A.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Chaperone-mediated native folding of a beta-scorpion toxin in the periplasm of Escherichia coli.
Authors: O'Reilly, A.O. / Cole, A.R. / Lopes, J.L. / Lampert, A. / Wallace, B.A.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 20, 2024Group: 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 / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-insect excitatory toxin Bj-xtrIT
B: Beta-insect excitatory toxin Bj-xtrIT
C: Beta-insect excitatory toxin Bj-xtrIT
D: Beta-insect excitatory toxin Bj-xtrIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2537
Polymers37,7594
Non-polymers4953
Water6,107339
1
A: Beta-insect excitatory toxin Bj-xtrIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5902
Polymers9,4401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-insect excitatory toxin Bj-xtrIT


Theoretical massNumber of molelcules
Total (without water)9,4401
Polymers9,4401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-insect excitatory toxin Bj-xtrIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5902
Polymers9,4401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-insect excitatory toxin Bj-xtrIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6342
Polymers9,4401
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.870, 88.560, 183.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-101-

PGE

21A-286-

HOH

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Components

#1: Protein
Beta-insect excitatory toxin Bj-xtrIT / Bjxtr-IT / BjxtrIT


Mass: 9439.647 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hottentotta judaicus (scorpion) / Gene: XTRIT / Production host: Escherichia coli (E. coli) / References: UniProt: P56637
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M NaCl, Bis-Tris, 29% PEG 3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2012
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→44.28 Å / Num. all: 26392 / Num. obs: 26392 / % possible obs: 69.23 % / Observed criterion σ(F): 1.48 / Observed criterion σ(I): 1.22 / Biso Wilson estimate: 20.05 Å2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.22 / % possible all: 9.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.28 Å / Cor.coef. Fo:Fc: 0.9112 / Cor.coef. Fo:Fc free: 0.8947 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1334 5.05 %RANDOM
Rwork0.1969 ---
obs0.1986 26392 69.23 %-
all-26392 --
Displacement parametersBiso mean: 24.28 Å2
Baniso -1Baniso -2Baniso -3
1--5.4693 Å20 Å20 Å2
2--3.3091 Å20 Å2
3---2.1602 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 33 339 2599
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957906HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d942SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes640HARMONIC5
X-RAY DIFFRACTIONt_it4399HARMONIC20
X-RAY DIFFRACTIONt_nbd17SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.7→1.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2626 35 4.94 %
Rwork0.2111 673 -
all0.2134 708 -
obs--69.23 %

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