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- PDB-6imf: Crystal structure of TOXIN/ANTITOXIN complex -

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Basic information

Entry
Database: PDB / ID: 6imf
TitleCrystal structure of TOXIN/ANTITOXIN complex
Components
  • Cysteine-rich venom protein triflin
  • Small serum protein 2
KeywordsTOXIN/ANTITOXIN / COMPLEX / ANTITOXIN / TOXIN-ANTITOXIN COMPLEX / TOXIN
Function / homology
Function and homology information


calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Beta-microseminoprotein / Beta-microseminoprotein (PSP-94) / Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site ...Beta-microseminoprotein / Beta-microseminoprotein (PSP-94) / Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small serum protein 2 / Cysteine-rich venom protein triflin
Similarity search - Component
Biological speciesProtobothrops flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShioi, N. / Tadokoro, T. / Shioi, S. / Hu, Y. / Kurahara, L.H. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. ...Shioi, N. / Tadokoro, T. / Shioi, S. / Hu, Y. / Kurahara, L.H. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. / Maenaka, K. / Terada, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22121007 Japan
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake.
Authors: Shioi, N. / Tadokoro, T. / Shioi, S. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. / Terada, S. / Maenaka, K.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine-rich venom protein triflin
B: Small serum protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4386
Polymers36,9672
Non-polymers4724
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-8 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.166, 48.113, 75.028
Angle α, β, γ (deg.)90.00, 102.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cysteine-rich venom protein triflin / CRVP


Mass: 24826.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: Q8JI39
#2: Protein Small serum protein 2 / SSP-2


Mass: 12140.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: A7VN14
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: AMMONIUM SULPHATE, MES, PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 17522 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.127 / Net I/σ(I): 11.488
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.434 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WVR AND 3IX0

1wvr

3ix0


Resolution: 2.3→39.64 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.69
RfactorNum. reflection% reflection
Rfree0.219 884 5.05 %
Rwork0.186 --
obs0.187 17519 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 30 84 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022411
X-RAY DIFFRACTIONf_angle_d0.5153245
X-RAY DIFFRACTIONf_dihedral_angle_d10.445885
X-RAY DIFFRACTIONf_chiral_restr0.021339
X-RAY DIFFRACTIONf_plane_restr0.002420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2956-2.43940.28891430.2262706X-RAY DIFFRACTION99
2.4394-2.62770.27961710.21112752X-RAY DIFFRACTION100
2.6277-2.8920.23451410.2052756X-RAY DIFFRACTION100
2.892-3.31030.23021340.19232774X-RAY DIFFRACTION100
3.3103-4.170.18461330.16752801X-RAY DIFFRACTION100
4.17-39.64620.18991620.16822846X-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)
14.85922.46230.86984.81140.54742.3745-0.03620.25470.2007-0.58-0.09060.2683-0.1737-0.170.09810.26520.06250.00760.17-0.01470.172117.465749.20794.6447
25.60231.111-5.73311.0574-1.20866.1871-0.54790.2059-0.9419-0.21540.05120.17541.0261-0.14660.56120.2725-0.01330.01210.1652-0.06730.346714.800534.085812.499
36.45940.7378-3.05542.681-0.1383.7495-0.1264-0.0881-0.22450.1041-0.03030.13410.30880.08720.20270.31220.02220.00060.1561-0.00380.211220.461736.501519.2702
46.55122.1457-2.24222.57740.88293.42210.2607-0.2470.12590.0115-0.33710.5109-0.1136-0.5945-0.06040.1630.0117-0.01930.291-0.04460.29447.470446.720415.5864
51.48940.5196-0.12632.0758-0.20022.37770.0599-0.08730.0391-0.0034-0.12510.0077-0.25830.00570.0570.17090.01130.01430.13210.01150.189621.474451.350813.7586
61.4738-1.4688-0.21456.15340.15398.41810.11290.09990.31260.6036-0.338-1.0180.51280.860.47110.4550.2252-0.1290.75990.02620.766545.576137.974115.8969
71.50770.4754-0.83623.49761.25382.3322-0.00050.25690.72-0.2632-0.2955-2.11850.63171.53530.17640.37180.15920.10640.60910.05630.687142.867443.92068.1678
87.3719-5.06713.14066.6542-2.95086.4161-0.9084-1.11490.75730.84290.0446-0.8382-0.53180.87370.85940.3159-0.0441-0.070.5250.07430.346631.603343.164127.6561
97.47392.33440.86181.3714-1.61535.6821-0.6025-0.31450.72620.95550.30740.04110.73630.13510.30950.55940.06250.00070.2549-0.05710.310329.274438.922942.4392
107.24-4.78274.07487.3609-5.15123.7767-0.1028-0.0396-0.0390.04710.27180.3191-0.0423-0.2458-0.19640.3519-0.0127-0.00140.23160.01260.172823.980939.312534.2397
119.1601-4.62743.71132.7891-1.45464.5111-0.2392-0.4182-0.2543-0.02670.240.2631-0.0428-0.0557-0.03920.2895-0.02290.05120.20470.02130.229715.669745.010825.1594
128.9906-1.21476.57367.7251-1.25324.8727-0.0287-0.6647-0.1872-0.31060.07360.3361-0.1977-0.8652-0.03060.2450.01210.05210.3253-0.03950.20064.755552.85929.9888
133.6973-2.56082.56115.3663-4.63175.4280.1723-0.6061-0.37010.1253-0.01542.2929-1.3557-2.574-0.05220.5720.25810.0560.9891-0.15730.6783-5.327357.193628.5518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 42 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 43 THROUGH 55 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 56 THROUGH 73 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 74 THROUGH 85 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 86 THROUGH 184 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 185 THROUGH 209 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 210 THROUGH 221 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 18 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 19 THROUGH 28 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 29 THROUGH 46 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 47 THROUGH 64 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 65 THROUGH 80 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 81 THROUGH 89 )

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