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- PDB-9ybe: Rana catesbeiana saxiphilin mutant - F561A:STX (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 9ybe
TitleRana catesbeiana saxiphilin mutant - F561A:STX (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 / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Chem-9SL / Saxiphilin
Similarity search - Component
Biological speciesAquarana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, Z. / Zakrzewska, 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: Rana catesbeiana saxiphilin mutant - F561A:STX (co-crystal)
Authors: Chen, Z. / Zakrzewska, S. / Minor, D.L.
History
DepositionSep 17, 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
B: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,9034
Polymers188,3042
Non-polymers5992
Water5,152286
1
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4512
Polymers94,1521
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4512
Polymers94,1521
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.062, 105.111, 253.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Saxiphilin / SAX


Mass: 94152.211 Da / Num. of mol.: 2 / Mutation: F561A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquarana catesbeiana (American bullfrog)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P31226
#2: Chemical ChemComp-9SL / [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate / Saxitoxin


Mass: 299.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N7O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 2.35→48.54 Å / Num. obs: 107521 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 2.35→2.38 Å / Num. unique obs: 5258 / CC1/2: 0.599

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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: 2.35→48.54 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 5409 5.04 %
Rwork0.2396 --
obs0.2414 107391 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12754 0 21 286 13061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313032
X-RAY DIFFRACTIONf_angle_d0.55817602
X-RAY DIFFRACTIONf_dihedral_angle_d17.5044887
X-RAY DIFFRACTIONf_chiral_restr0.041914
X-RAY DIFFRACTIONf_plane_restr0.0042295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.43911660.42713370X-RAY DIFFRACTION100
2.38-2.40.40021750.42013363X-RAY DIFFRACTION100
2.4-2.430.46591610.42673352X-RAY DIFFRACTION100
2.43-2.460.45881820.40183375X-RAY DIFFRACTION100
2.46-2.50.43761830.3913369X-RAY DIFFRACTION100
2.5-2.530.44251900.38063343X-RAY DIFFRACTION100
2.53-2.570.42291740.37773352X-RAY DIFFRACTION100
2.57-2.610.39311800.35513369X-RAY DIFFRACTION100
2.61-2.650.40811710.35473367X-RAY DIFFRACTION100
2.65-2.690.39731790.34793386X-RAY DIFFRACTION100
2.69-2.740.40552040.35313331X-RAY DIFFRACTION100
2.74-2.790.38291700.34263380X-RAY DIFFRACTION100
2.79-2.840.41141870.33223379X-RAY DIFFRACTION100
2.84-2.90.37592000.30323325X-RAY DIFFRACTION100
2.9-2.960.32171830.28383378X-RAY DIFFRACTION100
2.96-3.030.29841680.27633404X-RAY DIFFRACTION100
3.03-3.110.35391700.28183402X-RAY DIFFRACTION100
3.11-3.190.32241690.28193407X-RAY DIFFRACTION100
3.19-3.280.32121770.28673357X-RAY DIFFRACTION100
3.28-3.390.30021910.27763408X-RAY DIFFRACTION100
3.39-3.510.3221830.25463376X-RAY DIFFRACTION100
3.51-3.650.29511900.23623415X-RAY DIFFRACTION100
3.65-3.820.2481660.21983414X-RAY DIFFRACTION100
3.82-4.020.24611860.21543406X-RAY DIFFRACTION100
4.02-4.270.25931750.20723414X-RAY DIFFRACTION100
4.27-4.60.22511700.19833466X-RAY DIFFRACTION100
4.6-5.060.22921790.19013455X-RAY DIFFRACTION100
5.06-5.790.25271900.21563446X-RAY DIFFRACTION100
5.79-7.290.23131890.22153515X-RAY DIFFRACTION100
7.29-48.540.18162010.16373658X-RAY DIFFRACTION100

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