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- PDB-3vts: Crystal structure of a three finger toxin from snake venom -

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Basic information

Entry
Database: PDB / ID: 3vts
TitleCrystal structure of a three finger toxin from snake venom
ComponentsCytotoxin 1
KeywordsTOXIN / Three finger toxin / Venom toxin
Function / homology
Function and homology information


regulation of blood pressure / toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Three-finger hemachatoxin
Similarity search - Component
Biological speciesHemachatus haemachatus (ringhals)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Plos One / Year: 2012
Title: Identification and structural characterization of a new three-finger toxin hemachatoxin from Hemachatus haemachatus venom.
Authors: Girish, V.M. / Kumar, S. / Joseph, L. / Jobichen, C. / Kini, R.M. / Sivaraman, J.
History
DepositionJun 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 1
B: Cytotoxin 1


Theoretical massNumber of molelcules
Total (without water)13,7172
Polymers13,7172
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.718, 50.057, 57.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:61 )
211CHAIN B AND (RESSEQ 1:61 )

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Components

#1: Protein Cytotoxin 1 / Hemolytic protein 12B / Three finger toxin


Mass: 6858.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemachatus haemachatus (ringhals) / References: UniProt: B3EWH9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHOR DEPOSITED SEQUENCE OF THIS PROTEIN AS THE CODE B3EWH9 BUT IT DOES NOT APPEAR IN TE ...THE AUTHOR DEPOSITED SEQUENCE OF THIS PROTEIN AS THE CODE B3EWH9 BUT IT DOES NOT APPEAR IN TE SEQUENCE DATABASE YET.

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 150mM ammonium acetate, 100mM sodium acetate, 25% polyethylene glycol 4000 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.426→30.112 Å / Num. all: 5639 / Num. obs: 5614 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TGX

1tgx


Resolution: 2.426→30.112 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 573 10.21 %
Rwork0.2322 --
obs0.2373 5614 96.63 %
all-5639 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.328 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9401 Å20 Å2-0 Å2
2--4.5662 Å2-0 Å2
3----5.4669 Å2
Refinement stepCycle: LAST / Resolution: 2.426→30.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 0 49 987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008960
X-RAY DIFFRACTIONf_angle_d1.3771272
X-RAY DIFFRACTIONf_dihedral_angle_d13.951392
X-RAY DIFFRACTIONf_chiral_restr0.088150
X-RAY DIFFRACTIONf_plane_restr0.006154
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A469X-RAY DIFFRACTIONPOSITIONAL
12B469X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4261-2.67020.39161390.3162124297
2.6702-3.05620.33431480.2594127199
3.0562-3.84930.32121380.2437126397
3.8493-30.11470.20821480.1914126593
Refinement TLS params.Method: refined / Origin x: 61.4575 Å / Origin y: 56.864 Å / Origin z: 9.017 Å
111213212223313233
T0.1738 Å20.0037 Å2-0.0101 Å2-0.2887 Å20.0331 Å2--0.1768 Å2
L1.9536 °2-0.4658 °2-0.2144 °2-1.1002 °20.1753 °2--1.2418 °2
S-0.1041 Å °-0.0023 Å °-0.0502 Å °0.0104 Å °0.0572 Å °0.0982 Å °-0.0512 Å °-0.0039 Å °0.0483 Å °
Refinement TLS groupSelection details: ALL

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