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- PDB-8v67: Nanorana parkeri saxiphilin:C1 (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 8v67
TitleNanorana parkeri saxiphilin:C1 (co-crystal)
ComponentsSaxiphilin
KeywordsANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin
Function / homology
Function and homology information


recycling endosome / antibacterial humoral response / iron ion transport / early endosome / extracellular space / plasma membrane
Similarity search - Function
Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesNanorana parkeri (frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZakrzewska, S. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HDTRA-1-19-1-0040 United States
Department of Defense (DOD, United States)HDTRA-1-21-1-10011 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for saxitoxin congener binding and neutralization by anuran saxiphilins.
Authors: Zakrzewska, S. / Nixon, S.A. / Chen, Z. / Hajare, H.S. / Park, E.R. / Mulcahy, J.V. / Arlinghaus, K.M. / Neu, E. / Konovalov, K. / Provasi, D. / Leighfield, T.A. / Filizola, M. / Du Bois, J. / Minor Jr., D.L.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4173
Polymers94,7041
Non-polymers7142
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)229.785, 229.785, 67.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Saxiphilin


Mass: 94703.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanorana parkeri (frog) / Gene: XM_018555331.1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A9X9ZA84
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-YH9 / ({[(3aS,4R,7R,9R,10aS)-2,6-diamino-10,10-dihydroxy-9-(sulfooxy)-3a,4,9,10-tetrahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)sulfamic acid


Mass: 475.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N7O11S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, C1&C2:NpSxph molar ratio 1.2:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11614 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11614 Å / Relative weight: 1
ReflectionResolution: 1.9→43.43 Å / Num. obs: 104543 / % possible obs: 99.92 % / Redundancy: 30.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2557 / Net I/σ(I): 6.51
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 10419 / CC1/2: 0.356 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.43 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 2007 1.92 %
Rwork0.2065 --
obs0.207 104463 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6362 0 46 291 6699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096577
X-RAY DIFFRACTIONf_angle_d1.0298903
X-RAY DIFFRACTIONf_dihedral_angle_d8.081905
X-RAY DIFFRACTIONf_chiral_restr0.062952
X-RAY DIFFRACTIONf_plane_restr0.0091163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.46161450.42057304X-RAY DIFFRACTION99
1.95-20.36281430.34967314X-RAY DIFFRACTION100
2-2.060.3231440.3157280X-RAY DIFFRACTION100
2.06-2.130.33031440.37351X-RAY DIFFRACTION100
2.13-2.20.31581430.29757325X-RAY DIFFRACTION100
2.2-2.290.31381450.28247300X-RAY DIFFRACTION100
2.29-2.390.29251430.26067332X-RAY DIFFRACTION100
2.39-2.520.26981450.23467273X-RAY DIFFRACTION100
2.52-2.680.24021440.24897336X-RAY DIFFRACTION100
2.68-2.880.2761430.22467337X-RAY DIFFRACTION100
2.88-3.170.2541430.23617298X-RAY DIFFRACTION100
3.18-3.630.22551420.20047342X-RAY DIFFRACTION100
3.63-4.580.1951430.17167334X-RAY DIFFRACTION100
4.58-43.430.17111400.15497330X-RAY DIFFRACTION100

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