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- PDB-8d6t: Rana catesbeiana saxiphilin mutant - Y558I:STX (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 8d6t
TitleRana catesbeiana saxiphilin mutant - Y558I: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 / 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 / Transferrin-like domain / Transferrin / Transferrin-like domain profile. ...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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9SL / CACODYLATE ION / Saxiphilin
Similarity search - Component
Biological speciesLithobates catesbeianus (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Z. / Zakrzewska, 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: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family.
Authors: Chen, Z. / Zakrzewska, S. / Hajare, H.S. / Alvarez-Buylla, A. / Abderemane-Ali, F. / Bogan, M. / Ramirez, D. / O'Connell, L.A. / Du Bois, J. / Minor Jr., D.L.
History
DepositionJun 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Saxiphilin
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,22610
Polymers187,8062
Non-polymers1,4218
Water14,304794
1
B: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6135
Polymers93,9031
Non-polymers7104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6135
Polymers93,9031
Non-polymers7104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.026, 107.812, 253.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Saxiphilin / SAX


Mass: 93902.992 Da / Num. of mol.: 2 / Mutation: Y558I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates catesbeianus (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: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 27% 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: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.15→47.5 Å / Num. obs: 142848 / % possible obs: 99.5 % / Redundancy: 12.2 % / Biso Wilson estimate: 44.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.2
Reflection shellResolution: 2.15→2.19 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6596 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O0F

6o0f


Resolution: 2.15→47.5 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 7099 4.98 %
Rwork0.2073 135555 -
obs0.2086 142654 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.8 Å2 / Biso mean: 69.0074 Å2 / Biso min: 29.99 Å2
Refinement stepCycle: final / Resolution: 2.15→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12622 0 72 794 13488
Biso mean--88.02 62.87 -
Num. residues----1636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.170.47212350.40574095433093
2.17-2.20.4162520.39164301455396
2.2-2.230.39782210.35774426464798
2.23-2.260.34962300.32584447467799
2.26-2.280.32372180.30644964714100
2.28-2.320.34132180.304545134731100
2.32-2.350.28992300.288744924722100
2.35-2.380.29252430.262344624705100
2.38-2.420.32562640.258244524716100
2.42-2.460.28982370.247945644801100
2.46-2.50.30342540.238444654719100
2.5-2.550.25622050.229745104715100
2.55-2.60.26352270.224745314758100
2.6-2.650.28172380.230145104748100
2.65-2.710.26662280.224545114739100
2.71-2.770.28042290.231745374766100
2.77-2.840.27572130.232445544767100
2.84-2.920.25062350.23445384773100
2.92-30.26632460.235945204766100
3-3.10.26072270.23145454772100
3.1-3.210.22472460.2245274773100
3.21-3.340.24822540.217245124766100
3.34-3.490.23812510.208445544805100
3.49-3.680.22762480.192845534801100
3.68-3.910.20422240.182545804804100
3.91-4.210.19352560.171645694825100
4.21-4.630.18292190.162646374856100
4.63-5.30.18412710.161946044875100
5.3-6.670.2142100.19847114921100
6.68-47.50.1942700.17524839510999
Refinement TLS params.Method: refined / Origin x: -48.5321 Å / Origin y: 24.4613 Å / Origin z: 31.9826 Å
111213212223313233
T0.309 Å2-0.0191 Å20.0226 Å2-0.5564 Å2-0.0065 Å2--0.2781 Å2
L0.252 °2-0.0151 °20.0794 °2-0.2327 °2-0.1605 °2--0.9611 °2
S-0.0165 Å °-0.0374 Å °-0.0236 Å °0.0548 Å °-0.0129 Å °-0.0109 Å °-0.0773 Å °0.1157 Å °0.0362 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB5 - 832
2X-RAY DIFFRACTION1allB901 - 903
3X-RAY DIFFRACTION1allA5 - 832
4X-RAY DIFFRACTION1allA901 - 908
5X-RAY DIFFRACTION1allS515 - 532
6X-RAY DIFFRACTION1allD1 - 277

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