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- PDB-4gv5: X-ray structure of crotamine, a cell-penetrating peptide from the... -

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Basic information

Entry
Database: PDB / ID: 4gv5
TitleX-ray structure of crotamine, a cell-penetrating peptide from the Brazilian snake Crotalus durissus terrificus
ComponentsCrotamine Ile-19
KeywordsTOXIN / alpha helix & beta sheet / Ion channel inhibitor / antibacterial peptide / Extracellular region
Function / homology
Function and homology information


envenomation resulting in occlusion of the pore of voltage-gated potassium channel in another organism / potassium channel regulator activity / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Myotoxin / Myotoxin, crotamine / Myotoxins signature. / Myotoxins family profile. / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Crotamine / Crotamine
Similarity search - Component
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCoronado, M.A. / Gabdulkhakov, A. / Georgieva, D. / Sankaran, B. / Murakami, M.T. / Arni, R.K. / Betzel, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus.
Authors: Coronado, M.A. / Gabdulkhakov, A. / Georgieva, D. / Sankaran, B. / Murakami, M.T. / Arni, R.K. / Betzel, C.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crotamine Ile-19
B: Crotamine Ile-19
C: Crotamine Ile-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,59814
Polymers14,7093
Non-polymers88911
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Crotamine Ile-19
B: Crotamine Ile-19
C: Crotamine Ile-19
hetero molecules

A: Crotamine Ile-19
B: Crotamine Ile-19
C: Crotamine Ile-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,19528
Polymers29,4176
Non-polymers1,77822
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area8800 Å2
ΔGint-129 kcal/mol
Surface area14530 Å2
MethodPISA
3
B: Crotamine Ile-19
hetero molecules

A: Crotamine Ile-19
C: Crotamine Ile-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,59814
Polymers14,7093
Non-polymers88911
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation6_655-x+1,-y+1/2,z1
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-67 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.922, 74.330, 80.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11C-212-

HOH

21C-213-

HOH

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Components

#1: Protein/peptide Crotamine Ile-19 / CRO_Ile-19


Mass: 4902.878 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P01475, UniProt: Q9PWF3*PLUS
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.2 M sodium thiocyanate, 1.9 M ammonium sulphate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.12
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 22612 / Num. obs: 20890 / % possible obs: 97.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.493 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22537 1121 5.1 %RANDOM
Rwork0.16694 ---
obs0.1699 20890 98.24 %-
all-16628 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å20 Å2
2---0.86 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 51 62 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0191116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8561.9751471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.80221.53839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4315221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.576156
X-RAY DIFFRACTIONr_chiral_restr0.1960.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021784
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr11.82631116
X-RAY DIFFRACTIONr_sphericity_free27.031531
X-RAY DIFFRACTIONr_sphericity_bonded36.11251122
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.691 63 -
Rwork0.55 1125 -
obs--78.06 %

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