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- PDB-4lft: Structure of alpha-elapitoxin-Dpp2d isolated from Black Mamba (De... -

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Basic information

Entry
Database: PDB / ID: 4lft
TitleStructure of alpha-elapitoxin-Dpp2d isolated from Black Mamba (Dendroaspis polylepis) venom
ComponentsAlpha-elapitoxin-Dpp2a
KeywordsTOXIN / Long neurotoxin / three-finger-toxin / disulfide-rich / acetylcholine receptor inhibitor activity / expressed by the venom gland
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Alpha-elapitoxin-Dpp2a
Similarity search - Component
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, C.I.A. / Reeks, T. / Lewis, R.J. / Alewood, P.F. / Durek, T.
CitationJournal: Biochemistry / Year: 2014
Title: Isolation and Structural and Pharmacological Characterization of alpha-Elapitoxin-Dpp2d, an Amidated Three Finger Toxin from Black Mamba Venom.
Authors: Wang, C.I. / Reeks, T. / Vetter, I. / Vergara, I. / Kovtun, O. / Lewis, R.J. / Alewood, P.F. / Durek, T.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-elapitoxin-Dpp2a
B: Alpha-elapitoxin-Dpp2a


Theoretical massNumber of molelcules
Total (without water)16,0272
Polymers16,0272
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alpha-elapitoxin-Dpp2a


Theoretical massNumber of molelcules
Total (without water)8,0131
Polymers8,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Alpha-elapitoxin-Dpp2a


Theoretical massNumber of molelcules
Total (without water)8,0131
Polymers8,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.595, 38.270, 39.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-elapitoxin-Dpp2a / Alpha-EPTX-Dpp2a / Long neurotoxin 1 / Neurotoxin gamma / Toxin VN1


Mass: 8013.313 Da / Num. of mol.: 2 / Fragment: unp residues 65-136 / Source method: isolated from a natural source
Details: Isolated from crude venom using cation-exchange chromatography and reversed-phase chromatography.
Source: (natural) Dendroaspis polylepis polylepis (black mamba)
References: UniProt: P01396
#2: Water ChemComp-HOH / water / Alpha-EPTX-Dpp2a / Long neurotoxin 1 / Neurotoxin gamma / Toxin VN1


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS HAVE DEPOSITED A NEW ALPHA ELAPITOCIN DPP2D SEQUENCE IN UNIPROT WITH THE ASSIGNED ACCESSION ...AUTHORS HAVE DEPOSITED A NEW ALPHA ELAPITOCIN DPP2D SEQUENCE IN UNIPROT WITH THE ASSIGNED ACCESSION NUMBER C0HJD7

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein was dissolved in 2mM HCl, 5 mg/mL. reservoir: 0.1M TRIS-HCL, 2% (v/v) dioxane, 65% (v/v) 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 24, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→27.46 Å / Num. all: 121995 / Num. obs: 22047 / % possible obs: 92.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.53 % / Biso Wilson estimate: 23.903 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.2
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.9 / % possible all: 74.79

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NTN

1ntn


Resolution: 1.7→27.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.917 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22371 848 5 %RANDOM
Rwork0.1978 ---
all0.19916 22047 --
obs0.19916 15981 92.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.903 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 133 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021066
X-RAY DIFFRACTIONr_bond_other_d0.0010.021013
X-RAY DIFFRACTIONr_angle_refined_deg2.2671.9511439
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0172333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1455136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.28642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.195157
X-RAY DIFFRACTIONr_chiral_restr0.1450.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5082.049544
X-RAY DIFFRACTIONr_mcbond_other2.5032.049543
X-RAY DIFFRACTIONr_mcangle_it3.4523.076677
X-RAY DIFFRACTIONr_mcangle_other3.453.074678
X-RAY DIFFRACTIONr_scbond_it3.4862.451522
X-RAY DIFFRACTIONr_scbond_other3.4832.45523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2923.485762
X-RAY DIFFRACTIONr_long_range_B_refined7.31517.8591208
X-RAY DIFFRACTIONr_long_range_B_other7.01517.2861164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 45 -
Rwork0.25 946 -
obs-946 74.79 %

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