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- PDB-8d6o: Nanorana parkeri saxiphilin:F-STX (soaked) -

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Basic information

Entry
Database: PDB / ID: 8d6o
TitleNanorana parkeri saxiphilin:F-STX (soaked)
ComponentsSaxiphilin
KeywordsANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin
Function / homologyChem-QDX
Function and homology information
Biological speciesNanorana parkeri (frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZakrzewska, S. / Chen, Z. / 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 30, 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
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6993
Polymers94,7041
Non-polymers9952
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.186, 229.186, 67.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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)
#2: Chemical ChemComp-QDX / (2P)-4-({6-[({[(3aS,4R,7R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)amino]hexyl}carbamoyl)-2-{[4aP,9(9a)P]-6-hydroxy-3-oxo-3H-xanthen-9-yl}benzoic acid


Mass: 756.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H40N8O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsMALTFHTALYFTIVGLSFAASDA is a Signal Peptide. aSNSLEVLFQ is a linker sequence.

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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: 3.59 Å3/Da / Density % sol: 65.78 %
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, 1 mM (final concentration) F-STX was added during soaking

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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: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.2→43.31 Å / Num. obs: 66898 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 55.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07078 / Net I/σ(I): 19.64
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 1.35 / Num. unique obs: 6682 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8D6G

8d6g


Resolution: 2.2→43.31 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 3301 4.94 %
Rwork0.1968 63588 -
obs0.199 66889 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.21 Å2 / Biso mean: 71.9182 Å2 / Biso min: 35.15 Å2
Refinement stepCycle: final / Resolution: 2.2→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 60 161 6567
Biso mean--87.47 59.28 -
Num. residues----819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.41921340.382426572791100
2.23-2.260.41911090.356326552764100
2.26-2.30.37231220.330526632785100
2.3-2.340.35061480.305326582806100
2.34-2.380.3211560.294726142770100
2.38-2.420.35821190.273126672786100
2.42-2.470.31091440.278226252769100
2.47-2.520.29621450.258826602805100
2.52-2.570.3351340.25926712805100
2.57-2.630.32461540.262426612815100
2.63-2.70.33191380.270526472785100
2.7-2.770.37271380.261426122750100
2.77-2.850.32411680.249526662834100
2.85-2.950.26911280.245226442772100
2.95-3.050.28561140.248226902804100
3.05-3.170.28171340.238626372771100
3.17-3.320.26071450.236526462791100
3.32-3.490.26411570.218626252782100
3.49-3.710.25111440.199426262770100
3.71-40.24051430.173326602803100
4-4.40.20481170.151526392756100
4.4-5.030.16121210.144326812802100
5.04-6.340.20981570.160426502807100
6.34-43.310.17041320.14062634276699

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