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- PDB-7qhi: Crystal structure of cytotoxin 13 from Naja naja, hexagonal form -

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Basic information

Entry
Database: PDB / ID: 7qhi
TitleCrystal structure of cytotoxin 13 from Naja naja, hexagonal form
ComponentsCytotoxin 13
KeywordsTOXIN / THREE-FINGER TOXIN / COBRA SNAKE VENOM / S-TTPE CYTOTOXIN
Function / homologySnake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Snake toxin-like superfamily / toxin activity / extracellular region / Cytotoxin 13
Function and homology information
Biological speciesNaja naja (Indian cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsSamygina, V.R. / Dubova, K.M. / Bourenkov, G. / Utkin, Y.N. / Dubovskii, P.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research16-04-01479 Russian Federation
CitationJournal: Toxins / Year: 2022
Title: Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling.
Authors: Dubovskii, P.V. / Dubova, K.M. / Bourenkov, G. / Starkov, V.G. / Konshina, A.G. / Efremov, R.G. / Utkin, Y.N. / Samygina, V.R.
History
DepositionDec 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Cytotoxin 13
BBB: Cytotoxin 13
CCC: Cytotoxin 13


Theoretical massNumber of molelcules
Total (without water)20,2693
Polymers20,2693
Non-polymers00
Water3,909217
1
AAA: Cytotoxin 13


  • defined by author
  • Evidence: gel filtration
  • 6.76 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6,7561
Polymers6,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Cytotoxin 13


  • defined by author
  • 6.76 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6,7561
Polymers6,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Cytotoxin 13


Theoretical massNumber of molelcules
Total (without water)6,7561
Polymers6,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.331, 109.331, 135.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11BBB-117-

HOH

21BBB-135-

HOH

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Components

#1: Protein Cytotoxin 13


Mass: 6756.275 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Naja naja (Indian cobra) / References: UniProt: A0A0U4N5W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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 % sol: 74.93 %
Crystal growTemperature: 273 K / Method: counter-diffusion / Details: Sodium chloride, K/NaPhosphate,MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21512 / % possible obs: 98.39 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1360

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RL5

1rl5


Resolution: 2.302→14.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.796 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2283 1034 4.807 %
Rwork0.1987 20478 -
all0.2 --
obs-21512 98.386 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.008 Å2-0.004 Å2-0 Å2
2---0.008 Å20 Å2
3---0.025 Å2
Refinement stepCycle: LAST / Resolution: 2.302→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 217 1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131425
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171416
X-RAY DIFFRACTIONr_angle_refined_deg2.0941.6651926
X-RAY DIFFRACTIONr_angle_other_deg1.3271.5913315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4745177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.60422.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97215285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.632156
X-RAY DIFFRACTIONr_chiral_restr0.10.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021500
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02246
X-RAY DIFFRACTIONr_nbd_refined0.2340.2289
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21305
X-RAY DIFFRACTIONr_nbtor_refined0.170.2683
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2736
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3350.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.20.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3250.211
X-RAY DIFFRACTIONr_nbd_other0.2340.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.216
X-RAY DIFFRACTIONr_mcbond_it2.1342.713717
X-RAY DIFFRACTIONr_mcbond_other2.1342.712716
X-RAY DIFFRACTIONr_mcangle_it3.6034.058891
X-RAY DIFFRACTIONr_mcangle_other3.6024.06892
X-RAY DIFFRACTIONr_scbond_it3.0483.063708
X-RAY DIFFRACTIONr_scbond_other3.0523.06705
X-RAY DIFFRACTIONr_scangle_it4.8634.4261035
X-RAY DIFFRACTIONr_scangle_other4.8644.4251034
X-RAY DIFFRACTIONr_lrange_it7.99932.8721578
X-RAY DIFFRACTIONr_lrange_other7.64832.4811535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.3610.338780.31292X-RAY DIFFRACTION89.484
2.361-2.4240.333640.3021425X-RAY DIFFRACTION97.7034
2.424-2.4920.329670.2781373X-RAY DIFFRACTION98.9011
2.492-2.5660.308690.2791353X-RAY DIFFRACTION99.7195
2.566-2.6480.235570.2411325X-RAY DIFFRACTION99.9277
2.648-2.7380.282700.2381282X-RAY DIFFRACTION99.9261
2.738-2.8380.278610.2111227X-RAY DIFFRACTION100
2.838-2.9490.272500.2091218X-RAY DIFFRACTION99.9212
2.949-3.0750.214610.1891147X-RAY DIFFRACTION99.8347
3.075-3.2180.196520.1791111X-RAY DIFFRACTION100
3.218-3.3830.223530.1751049X-RAY DIFFRACTION99.8188
3.383-3.5770.206580.1861006X-RAY DIFFRACTION99.9061
3.577-3.8090.209590.184946X-RAY DIFFRACTION99.9006
3.809-4.0920.189400.178905X-RAY DIFFRACTION99.8943
4.092-4.4490.176390.148835X-RAY DIFFRACTION100
4.449-4.920.149480.137767X-RAY DIFFRACTION100
4.92-5.5810.162340.176698X-RAY DIFFRACTION100
5.581-6.6090.283240.202625X-RAY DIFFRACTION99.8462
6.609-8.5480.18260.171514X-RAY DIFFRACTION99.4475
8.54-14.90.35240.241379X-RAY DIFFRACTION99.5062
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7030.6509-1.2711.1639-0.09761.18130.08080.09780.035-0.1037-0.0116-0.10860.0064-0.1392-0.06910.2526-0.0820.02880.11180.03180.0295-12.99362.999146.75
21.01011.0322-0.82852.1678-1.74162.28790.10090.22340.16230.13530.03450.09030.0581-0.1134-0.13530.1884-0.03080.00910.10450.06130.0453-11.90385.523146.797
31.34442.0922-0.03335.51051.0220.5327-0.06710.1738-0.3329-0.21810.3056-0.9617-0.0403-0.0176-0.23850.1369-0.06240.02820.0799-0.00520.23857.81483.598161.257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 60
2X-RAY DIFFRACTION2ALLBBB1 - 60
3X-RAY DIFFRACTION3ALLCCC1 - 60

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