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- PDB-9yat: Rana catesbeiana saxiphilin mutant - T563A -

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Basic information

Entry
Database: PDB / ID: 9yat
TitleRana catesbeiana saxiphilin mutant - T563A
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
Biological speciesAquarana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 - T563A
Authors: Chen, Z. / Zakrzewska, S. / Minor, D.L.
History
DepositionSep 16, 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


Theoretical massNumber of molelcules
Total (without water)188,3972
Polymers188,3972
Non-polymers00
Water3,081171
1
A: Saxiphilin


Theoretical massNumber of molelcules
Total (without water)94,1981
Polymers94,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Saxiphilin


Theoretical massNumber of molelcules
Total (without water)94,1981
Polymers94,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.302, 109.695, 253.139
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: 94198.281 Da / Num. of mol.: 2 / Mutation: T563A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.55 Å3/Da / Density % sol: 65.33 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 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: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.5→47.66 Å / Num. obs: 92708 / % possible obs: 99.2 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.53 Å / Num. unique obs: 4526 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.66 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 4725 5.1 %
Rwork0.2068 --
obs0.2088 92597 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12751 0 0 171 12922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213005
X-RAY DIFFRACTIONf_angle_d0.54117551
X-RAY DIFFRACTIONf_dihedral_angle_d14.1914870
X-RAY DIFFRACTIONf_chiral_restr0.041912
X-RAY DIFFRACTIONf_plane_restr0.0042288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.41231500.39382871X-RAY DIFFRACTION97
2.53-2.560.40331700.37932916X-RAY DIFFRACTION99
2.56-2.590.36871340.35372810X-RAY DIFFRACTION98
2.59-2.620.36911530.33752889X-RAY DIFFRACTION99
2.62-2.660.3331440.31832931X-RAY DIFFRACTION99
2.66-2.690.37631490.30932869X-RAY DIFFRACTION98
2.69-2.730.33891600.30392896X-RAY DIFFRACTION99
2.73-2.770.33881610.30882842X-RAY DIFFRACTION98
2.77-2.820.40571440.33082947X-RAY DIFFRACTION99
2.82-2.860.34691320.34532900X-RAY DIFFRACTION99
2.86-2.910.36781900.31532851X-RAY DIFFRACTION98
2.91-2.960.34531520.29192904X-RAY DIFFRACTION99
2.96-3.020.31731710.25462869X-RAY DIFFRACTION98
3.02-3.080.2861750.24382897X-RAY DIFFRACTION100
3.08-3.150.26051710.23052905X-RAY DIFFRACTION99
3.15-3.220.28491740.22652883X-RAY DIFFRACTION98
3.22-3.30.26051510.22772924X-RAY DIFFRACTION100
3.3-3.390.27661690.22522912X-RAY DIFFRACTION99
3.39-3.490.26361410.2312923X-RAY DIFFRACTION99
3.49-3.610.21271500.20012923X-RAY DIFFRACTION99
3.61-3.730.21361770.22934X-RAY DIFFRACTION99
3.73-3.880.24041590.18722931X-RAY DIFFRACTION99
3.88-4.060.23341710.18372957X-RAY DIFFRACTION99
4.06-4.270.24171460.1832939X-RAY DIFFRACTION100
4.27-4.540.19481490.16992994X-RAY DIFFRACTION100
4.54-4.890.19951630.1632966X-RAY DIFFRACTION99
4.89-5.380.22231720.17482992X-RAY DIFFRACTION100
5.38-6.160.24321520.20943018X-RAY DIFFRACTION100
6.16-7.760.21931370.20353080X-RAY DIFFRACTION100
7.76-47.660.18511580.14713199X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.2767 Å / Origin y: 29.2978 Å / Origin z: 31.5981 Å
111213212223313233
T0.4295 Å2-0.0458 Å2-0.0543 Å2-0.5495 Å2-0.0172 Å2--0.4458 Å2
L0.7001 °2-0.1015 °2-0.2713 °2-0.3757 °20.1875 °2--1.3175 °2
S-0.0302 Å °-0.1515 Å °0.0181 Å °0.0974 Å °0.0072 Å °0.0133 Å °0.174 Å °-0.0849 Å °0.0371 Å °
Refinement TLS groupSelection details: all

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