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- PDB-9bk6: Structure of B10_CYTX binder-complex -

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Basic information

Entry
Database: PDB / ID: 9bk6
TitleStructure of B10_CYTX binder-complex
Components
  • B10_CYTX binder
  • Cytotoxin 1
KeywordsDE NOVO PROTEIN/TOXIN / cytotoxins / protein design / diffusion / deep learning / DE NOVO PROTEIN / DE NOVO PROTEIN-TOXIN complex
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Naja pallida (red spitting cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBera, A.K. / Torres, S.V. / Kang, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: De novo designed proteins neutralize lethal snake venom toxins.
Authors: Vazquez Torres, S. / Benard Valle, M. / Mackessy, S.P. / Menzies, S.K. / Casewell, N.R. / Ahmadi, S. / Burlet, N.J. / Muratspahic, E. / Sappington, I. / Overath, M.D. / Rivera-de-Torre, E. / ...Authors: Vazquez Torres, S. / Benard Valle, M. / Mackessy, S.P. / Menzies, S.K. / Casewell, N.R. / Ahmadi, S. / Burlet, N.J. / Muratspahic, E. / Sappington, I. / Overath, M.D. / Rivera-de-Torre, E. / Ledergerber, J. / Laustsen, A.H. / Boddum, K. / Bera, A.K. / Kang, A. / Brackenbrough, E. / Cardoso, I.A. / Crittenden, E.P. / Edge, R.J. / Decarreau, J. / Ragotte, R.J. / Pillai, A.S. / Abedi, M. / Han, H.L. / Gerben, S.R. / Murray, A. / Skotheim, R. / Stuart, L. / Stewart, L. / Fryer, T.J.A. / Jenkins, T.P. / Baker, D.
History
DepositionApr 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B10_CYTX binder
B: Cytotoxin 1


Theoretical massNumber of molelcules
Total (without water)18,2312
Polymers18,2312
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-12 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.564, 63.663, 77.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein B10_CYTX binder


Mass: 11392.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Cytotoxin 1 / CTX-1 / Cardiotoxin gamma


Mass: 6838.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja pallida (red spitting cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: P01468
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6, 0.01 M Zinc chloride, 20% (w/v) PEG 6000 and 10 % (v/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 28, 2024 / Details: KB bimorph mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2→33.17 Å / Num. obs: 12102 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.64 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.041 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 864 / CC1/2: 0.929 / Rpim(I) all: 0.281 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXdev_5288refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.17 Å / SU ML: 0.1903 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.4279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 599 4.97 %
Rwork0.2496 11448 -
obs0.2514 12047 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.62 Å2
Refinement stepCycle: LAST / Resolution: 2→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 0 57 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211255
X-RAY DIFFRACTIONf_angle_d0.43781688
X-RAY DIFFRACTIONf_chiral_restr0.041197
X-RAY DIFFRACTIONf_plane_restr0.0039216
X-RAY DIFFRACTIONf_dihedral_angle_d13.3773499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.41671420.33012786X-RAY DIFFRACTION99.19
2.2-2.520.33611570.30592811X-RAY DIFFRACTION99.53
2.52-3.170.34571540.28132858X-RAY DIFFRACTION99.54
3.17-33.170.22271460.21342993X-RAY DIFFRACTION99.3

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