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- PDB-9y91: Nanorana parkeri saxiphilin:STX-C13-NBz (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 9y91
TitleNanorana parkeri saxiphilin:STX-C13-NBz (co-crystal)
ComponentsSaxiphilin
KeywordsANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin
Function / homology
Function and homology information


iron ion transport / recycling endosome / antibacterial humoral response / early endosome / : / 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: 1.95 Å
AuthorsZakrzewska, S. / Minor, D.L.
Funding support United States, 3items
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
Department of Defense (DOD, United States)HDTRA-1-23-1-0026 United States
CitationJournal: To Be Published
Title: Nanorana parkeri saxiphilin:STX-C13-Bzm (co-crystal)
Authors: Zakrzewska, S. / Minor, D.L.
History
DepositionSep 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3013
Polymers94,7041
Non-polymers5982
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.982, 228.982, 67.487
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: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-A1CTW / N-{[(2Z,3aS,4S,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl}benzamide


Mass: 359.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.6 Å3/Da / Density % sol: 65.79 %
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, STX-C13-NBz:NpSxph molar ratio 1.2:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.95→43.27 Å / Num. obs: 96135 / % possible obs: 99.93 % / Redundancy: 10.7 % / CC1/2: 0.999 / Net I/σ(I): 12.65
Reflection shellResolution: 1.95→1.97 Å / Num. unique obs: 3245 / CC1/2: 0.286

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.27 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 4750 4.94 %
Rwork0.1941 --
obs0.1955 96113 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 42 400 6805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096577
X-RAY DIFFRACTIONf_angle_d0.9298897
X-RAY DIFFRACTIONf_dihedral_angle_d17.7172471
X-RAY DIFFRACTIONf_chiral_restr0.057952
X-RAY DIFFRACTIONf_plane_restr0.0081164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.40281780.38863059X-RAY DIFFRACTION100
1.97-20.38181640.33883040X-RAY DIFFRACTION100
2-2.020.36111230.31293016X-RAY DIFFRACTION100
2.02-2.050.32511450.30743086X-RAY DIFFRACTION100
2.05-2.070.35631600.28393027X-RAY DIFFRACTION100
2.07-2.10.33671500.28113072X-RAY DIFFRACTION100
2.1-2.130.28211470.27493050X-RAY DIFFRACTION100
2.13-2.160.3011520.28493083X-RAY DIFFRACTION100
2.16-2.20.30581560.26163025X-RAY DIFFRACTION100
2.2-2.230.27521750.24813033X-RAY DIFFRACTION100
2.23-2.270.2511760.23063015X-RAY DIFFRACTION100
2.27-2.310.28551650.22353067X-RAY DIFFRACTION100
2.31-2.360.23651510.22623029X-RAY DIFFRACTION100
2.36-2.40.25021870.21073010X-RAY DIFFRACTION100
2.4-2.460.27811700.21573040X-RAY DIFFRACTION100
2.46-2.510.24591700.21043014X-RAY DIFFRACTION100
2.51-2.580.22151610.21653071X-RAY DIFFRACTION100
2.58-2.650.25911470.2233028X-RAY DIFFRACTION100
2.65-2.720.2631770.23413032X-RAY DIFFRACTION100
2.72-2.810.24711620.22433044X-RAY DIFFRACTION100
2.81-2.910.26711560.21893091X-RAY DIFFRACTION100
2.91-3.030.24651430.22683027X-RAY DIFFRACTION100
3.03-3.170.26391530.21373047X-RAY DIFFRACTION100
3.17-3.330.24861470.21633076X-RAY DIFFRACTION100
3.33-3.540.23831360.19733083X-RAY DIFFRACTION100
3.54-3.820.21281520.18143021X-RAY DIFFRACTION100
3.82-4.20.20271570.15853073X-RAY DIFFRACTION100
4.2-4.810.14231450.14243047X-RAY DIFFRACTION100
4.81-6.050.19451660.1573032X-RAY DIFFRACTION100
6.05-43.270.16411790.1553025X-RAY DIFFRACTION100

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