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- PDB-1jzb: Crystal Structure of Variant 2 Scorpion Toxin from Centruroides s... -

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Basic information

Entry
Database: PDB / ID: 1jzb
TitleCrystal Structure of Variant 2 Scorpion Toxin from Centruroides sculpturatus Ewing
ComponentsNEUROTOXIN 2
KeywordsTOXIN / scorpion toxin / noncrystallographic symmetry
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
Biological speciesCentruroides sculpturatus (bark scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsCook, W.J. / Zell, A. / Watt, D.D. / Ealick, S.E.
CitationJournal: Protein Sci. / Year: 2002
Title: Structure of variant 2 scorpion toxin from Centruroides sculpturatus Ewing.
Authors: Cook, W.J. / Zell, A. / Watt, D.D. / Ealick, S.E.
History
DepositionSep 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS CORRECT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROTOXIN 2


Theoretical massNumber of molelcules
Total (without water)7,1821
Polymers7,1821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.800, 48.800, 43.700
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 NEUROTOXIN 2


Mass: 7182.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Centruroides sculpturatus (bark scorpion) / References: UniProt: P01493
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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 2-methyl-2,4-pentanediol, CHES buffer, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Ealick, S.E., (1984) J. Biol. Chem., 259, 12081. / PH range low: 9.8 / PH range high: 8.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
233-36 %(v/v)MPD1reservoir
350 mMCHES1reservoirpH8.6-9.8

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: PICKER / Detector: DIFFRACTOMETER / Date: Jan 1, 1985
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 1609 / Num. obs: 1609 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.98 Å / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 100 Å

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→42.26 Å / Rfactor Rfree error: 0.031 / Data cutoff high absF: 125210.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 81 5 %RANDOM
Rwork0.233 ---
all-1609 --
obs-1609 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 122.39 Å2 / ksol: 0.582076 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å210.35 Å20 Å2
2---1.19 Å20 Å2
3---2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.81→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 0 0 498
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.121 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 8 3.1 %
Rwork0.283 252 -
obs--96.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.281
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3
X-RAY DIFFRACTIONc_scbond_it2.7
X-RAY DIFFRACTIONc_mcangle_it2.77
X-RAY DIFFRACTIONc_scangle_it3.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.283 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.283 / Num. reflection obs: 260 / Rfactor obs: 0.286

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