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- PDB-9y92: Nanorana parkeri saxiphilin:STX-C13-OBz (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 9y92
TitleNanorana parkeri saxiphilin:STX-C13-OBz (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: 1.9 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-OBz (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)95,3023
Polymers94,7041
Non-polymers5992
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)228.643, 228.643, 67.180
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-A1CTG / [(2Z,3aS,4R,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl benzoate


Mass: 360.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N6O4 / 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: 3.57 Å3/Da / Density % sol: 65.53 %
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-OBz: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: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.9→43.21 Å / Num. obs: 103144 / % possible obs: 99.93 % / Redundancy: 10.4 % / CC1/2: 0.999 / Net I/σ(I): 16.01
Reflection shellResolution: 1.9→1.92 Å / Num. unique obs: 3488 / CC1/2: 0.562

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.21 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 4988 4.84 %
Rwork0.1977 --
obs0.199 103129 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 42 400 6805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076568
X-RAY DIFFRACTIONf_angle_d0.7898883
X-RAY DIFFRACTIONf_dihedral_angle_d17.0812463
X-RAY DIFFRACTIONf_chiral_restr0.051951
X-RAY DIFFRACTIONf_plane_restr0.0071162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.44151630.43983325X-RAY DIFFRACTION100
1.92-1.940.43591590.3853259X-RAY DIFFRACTION100
1.94-1.970.39971700.36243303X-RAY DIFFRACTION100
1.97-1.990.32521750.31323270X-RAY DIFFRACTION100
1.99-2.020.31581350.30093239X-RAY DIFFRACTION99
2.02-2.050.30261770.28963245X-RAY DIFFRACTION100
2.05-2.080.32161380.26093300X-RAY DIFFRACTION100
2.08-2.110.26631850.25473250X-RAY DIFFRACTION100
2.11-2.140.26851450.24023265X-RAY DIFFRACTION100
2.14-2.170.28261730.24083306X-RAY DIFFRACTION100
2.17-2.210.29161640.24923261X-RAY DIFFRACTION100
2.21-2.250.26931730.23683289X-RAY DIFFRACTION100
2.25-2.30.27541660.23843231X-RAY DIFFRACTION100
2.3-2.340.27231960.24323265X-RAY DIFFRACTION100
2.34-2.390.30271840.24213266X-RAY DIFFRACTION100
2.39-2.450.3641700.25373236X-RAY DIFFRACTION100
2.45-2.510.2731870.23113253X-RAY DIFFRACTION100
2.51-2.580.25281730.22983312X-RAY DIFFRACTION100
2.58-2.650.24171840.23193217X-RAY DIFFRACTION100
2.65-2.740.31731790.22363279X-RAY DIFFRACTION100
2.74-2.840.27411690.23343263X-RAY DIFFRACTION100
2.84-2.950.29831340.24653286X-RAY DIFFRACTION100
2.95-3.090.27371290.23483318X-RAY DIFFRACTION100
3.09-3.250.22991650.21393279X-RAY DIFFRACTION100
3.25-3.450.25871780.20433247X-RAY DIFFRACTION100
3.45-3.720.22431410.19223323X-RAY DIFFRACTION100
3.72-4.090.18451630.16283263X-RAY DIFFRACTION100
4.09-4.680.16761660.14513268X-RAY DIFFRACTION100
4.68-5.90.16591590.1563282X-RAY DIFFRACTION100
5.9-43.210.16981880.15233241X-RAY DIFFRACTION100

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