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- PDB-1dq7: THREE-DIMENSIONAL STRUCTURE OF A NEUROTOXIN FROM RED SCORPION (BU... -

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Basic information

Entry
Database: PDB / ID: 1dq7
TitleTHREE-DIMENSIONAL STRUCTURE OF A NEUROTOXIN FROM RED SCORPION (BUTHUS TAMULUS) AT 2.2A RESOLUTION.
ComponentsNEUROTOXIN
KeywordsTOXIN / Red scorpion Neurotoxin
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 speciesMesobuthus tamulus (Indian red scorpion)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSharma, M. / Yadav, S. / Karthikeyan, S. / Kumar, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
CitationJournal: To be Published
Title: Three-dimensional Structure of a Neurotoxin from Red Scorpion (Buthus tamulus) at 2.2A Resolution
Authors: Sharma, M. / Yadav, S. / Karthikeyan, S. / Kumar, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
History
DepositionDec 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROTOXIN
B: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)14,0942
Polymers14,0942
Non-polymers00
Water1,63991
1
A: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)7,0471
Polymers7,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)7,0471
Polymers7,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.871, 21.001, 52.451
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEUROTOXIN


Mass: 7046.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mesobuthus tamulus (Indian red scorpion) / Secretion: VENOM / References: UniProt: P60277*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.2
Details: Protein Concentration 7.5mg/ml, Buffer Tris-Hcl 25mM, Percipitant 82% MPD, Additive 0.001 Cacl2, pH 7.2, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 71526 / Num. obs: 5166 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.186 / Num. unique all: 341 / % possible all: 59.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.2→14.92 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 453964.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 286 5.5 %RANDOM
Rwork0.201 ---
all0.212 71526 --
obs0.201 5176 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 115.1 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å2-3.16 Å2
2--7.05 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 91 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 33 5.5 %
Rwork0.354 562 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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