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- PDB-7qfc: Crystal structure of cytotoxin 13 from Naja naja, orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 7qfc
TitleCrystal structure of cytotoxin 13 from Naja naja, orthorhombic form
ComponentsCytotoxin 13
KeywordsTOXIN / THREE-FINGER TOXIN / COBRA SNAKE VENOM / S-TYPE CYTOTOXIN
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesNaja naja (Indian cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSamygina, V.R. / Dubova, K.M. / Bourenkov, G. / Utkin, Y.N. / Dubovskii, P.V.
Funding support1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research16-04-01479
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 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
DDD: Cytotoxin 13
EEE: Cytotoxin 13
FFF: Cytotoxin 13


Theoretical massNumber of molelcules
Total (without water)40,5386
Polymers40,5386
Non-polymers00
Water30617
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


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


  • 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
4
DDD: 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
5
EEE: 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
6
FFF: 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
Unit cell
Length a, b, c (Å)88.759, 97.175, 131.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cytotoxin 13


Mass: 6756.275 Da / Num. of mol.: 6 / 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.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: NaCl, sodium dihydrogen phosphate, 0.1M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18995 / % possible obs: 99.17 % / Redundancy: 6.3 % / Rsym value: 0.2 / Net I/σ(I): 1.8
Reflection shellResolution: 2.6→2.63 Å / Num. unique obs: 1199 / CC1/2: 0.89 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RL5

1rl5


Resolution: 2.6→14.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 29.095 / SU ML: 0.261 / Cross valid method: FREE R-VALUE / ESU R: 0.381 / ESU R Free: 0.275
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2547 874 4.918 %
Rwork0.2049 16898 -
all0.207 --
obs-17772 99.196 %
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: 93.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.722 Å20 Å2-0 Å2
2---0.371 Å20 Å2
3----0.351 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 17 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132850
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172832
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.6653852
X-RAY DIFFRACTIONr_angle_other_deg1.2781.5916630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2775354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.22522.596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.14815570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6061512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023000
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02492
X-RAY DIFFRACTIONr_nbd_refined0.2260.2535
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21308
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.21609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.27
X-RAY DIFFRACTIONr_nbd_other0.2210.294
X-RAY DIFFRACTIONr_mcbond_it4.3556.1311434
X-RAY DIFFRACTIONr_mcbond_other4.3536.1281433
X-RAY DIFFRACTIONr_mcangle_it6.9529.1761782
X-RAY DIFFRACTIONr_mcangle_other6.9519.181783
X-RAY DIFFRACTIONr_scbond_it4.8226.6181416
X-RAY DIFFRACTIONr_scbond_other4.7896.6081413
X-RAY DIFFRACTIONr_scangle_it7.6279.6982070
X-RAY DIFFRACTIONr_scangle_other7.6129.6952069
X-RAY DIFFRACTIONr_lrange_it11.1171.2892924
X-RAY DIFFRACTIONr_lrange_other11.10971.3272925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.47600.4531199X-RAY DIFFRACTION99.6044
2.665-2.7360.416530.4081199X-RAY DIFFRACTION100
2.736-2.8130.385620.3691123X-RAY DIFFRACTION99.6636
2.813-2.8960.408590.3271104X-RAY DIFFRACTION99.4867
2.896-2.9870.314570.2861091X-RAY DIFFRACTION99.7394
2.987-3.0880.277540.2511031X-RAY DIFFRACTION99.7243
3.088-3.1990.332440.2381024X-RAY DIFFRACTION99.8131
3.199-3.3230.226550.233963X-RAY DIFFRACTION99.8039
3.323-3.4630.281540.207962X-RAY DIFFRACTION99.9017
3.463-3.6220.212530.195879X-RAY DIFFRACTION99.8928
3.622-3.8060.303480.205864X-RAY DIFFRACTION100
3.806-4.020.288380.213828X-RAY DIFFRACTION100
4.02-4.2750.207440.175766X-RAY DIFFRACTION100
4.275-4.5870.176390.161738X-RAY DIFFRACTION100
4.587-4.9770.197420.151677X-RAY DIFFRACTION100
4.977-5.4890.314280.179646X-RAY DIFFRACTION100
5.489-6.1990.29280.202556X-RAY DIFFRACTION100
6.199-7.2830.189290.176501X-RAY DIFFRACTION100
7.283-9.2530.241130.172430X-RAY DIFFRACTION100
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)
12.1751.2363-0.85040.7402-0.49233.4576-0.09290.1130.235-0.05440.15140.05370.22710.1699-0.05850.31640.0017-0.08170.2501-0.03160.5666185.5437107.316160.6179
20.94490.1697-1.57333.8392-1.23473.6724-0.05910.0959-0.2281-0.19440.21920.0078-0.1398-0.1017-0.160.379-0.03090.03960.1772-0.0530.5424186.879684.7209153.3045
32.83731.68861.91182.02411.12351.3406-0.10440.0937-0.04920.06510.1589-0.34110.0077-0.0123-0.05450.3501-0.03710.04650.1414-0.01430.7487208.1796110.6103159.2932
45.33431.02542.0652.5980.31191.93520.2951-0.3798-0.0255-0.1423-0.04310.28990.1864-0.0583-0.25190.4219-0.064-0.08870.04830.06270.6675212.515288.0263165.5817
52.94410.08734.24483.04610.39916.4139-0.24720.09220.2151-0.5005-0.0278-0.1645-0.10780.20380.2750.489-0.05560.07450.32970.08830.395204.8412104.9409139.7479
62.3853-1.0329-0.27520.69921.18397.0301-0.67240.31270.03610.1516-0.00490.03660.4062-0.38740.67730.612-0.49770.11790.4625-0.07850.171179.286787.8171135.826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 60
2X-RAY DIFFRACTION2ALLBBB1 - 60
3X-RAY DIFFRACTION3ALLCCC1 - 60
4X-RAY DIFFRACTION4ALLDDD1 - 60
5X-RAY DIFFRACTION5ALLEEE1 - 60
6X-RAY DIFFRACTION6ALLFFF1 - 60

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