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- PDB-2a7t: Crystal Structure of a novel neurotoxin from Buthus tamalus at 2.... -

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Basic information

Entry
Database: PDB / ID: 2a7t
TitleCrystal Structure of a novel neurotoxin from Buthus tamalus at 2.2A resolution.
ComponentsNeurotoxin
KeywordsTOXIN / NOVEL / NEUROTOXIN / RED SCORPION
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / 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 ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / 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
Biological speciesMesobuthus tamulus (Indian red scorpion)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEthayathulla, A.S. / Sharma, M. / Saravanan, K. / Sharma, S. / Kaur, P. / Yadav, S. / Srinivasan, A. / Singh, T.P.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Crystal structure of a highly acidic neurotoxin from scorpion Buthus tamulus at 2.2A resolution reveals novel structural features.
Authors: Sharma, M. / Ethayathulla, A.S. / Jabeen, T. / Singh, N. / Sarvanan, K. / Yadav, S. / Sharma, S. / Srinivasan, A. / Singh, T.P.
History
DepositionJul 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotoxin
B: Neurotoxin


Theoretical massNumber of molelcules
Total (without water)14,0942
Polymers14,0942
Non-polymers00
Water2,108117
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 / Details: VENOM / Source: (natural) Mesobuthus tamulus (Indian red scorpion) / Strain: RED SCORPION / References: UniProt: P60277
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PROTEIN CONCENTRATION 7.5mg/ml, BUFFER TRIS-HCl 25 mM, PERCIPITANT 82% MPD, ADDITIVE 0.001 CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 1999 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: 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: 5462 / Num. obs: 5286 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15 Å2 / Rsym value: 0.094 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.186 / % possible all: 63

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→14.92 Å / Rfactor Rfree error: 0.021 / Data cutoff high absF: 645623.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 120 2.3 %RANDOM
Rwork0.205 ---
all0.206 5286 --
obs0.205 5166 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 1.23102 e/Å3
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å2-0.42 Å2
2--3 Å20 Å2
3----0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 117 1097
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_d25
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it2.541.5
X-RAY DIFFRACTIONc_mcangle_it3.672
X-RAY DIFFRACTIONc_scbond_it3.572
X-RAY DIFFRACTIONc_scangle_it5.012.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.191 15 2.5 %
Rwork0.27 580 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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