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- PDB-8d6g: Nanorana parkeri saxiphilin -

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Basic information

Entry
Database: PDB / ID: 8d6g
TitleNanorana parkeri saxiphilin
ComponentsSaxiphilin
KeywordsANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin
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 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1803
Polymers94,7041
Non-polymers4772
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.046, 229.046, 67.428
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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.59 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

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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: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.2→43.29 Å / Num. obs: 66067 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05218 / Net I/σ(I): 12.66
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 0.89 / Num. unique obs: 6127 / CC1/2: 0.465

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O0D

6o0d


Resolution: 2.2→43.29 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 3252 4.92 %
Rwork0.1889 62787 -
obs0.1912 66039 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.49 Å2 / Biso mean: 66.1513 Å2 / Biso min: 30.04 Å2
Refinement stepCycle: final / Resolution: 2.2→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 54 229 6646
Biso mean--88.84 55.62 -
Num. residues----821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.36281230.3572524264790
2.23-2.270.38191060.34342552265892
2.27-2.30.35531120.31662641275395
2.31-2.340.3741600.29922658281897
2.34-2.390.35821500.2782753290399
2.39-2.430.31041350.263827752910100
2.43-2.480.26031420.251128032945100
2.48-2.540.31881480.243727272875100
2.54-2.60.31051360.240328092945100
2.6-2.660.3281640.248927192883100
2.66-2.730.3451510.25827352886100
2.73-2.810.32461580.245427712929100
2.81-2.90.25841610.237727502911100
2.9-3.010.26571140.24122727284199
3.01-3.130.29661350.22982783291899
3.13-3.270.27991330.220928022935100
3.27-3.440.25131770.215326992876100
3.44-3.660.251490.194327582907100
3.66-3.940.2121390.163927922931100
3.94-4.340.19621290.1432761289099
4.34-4.960.15121250.1312768289399
4.96-6.250.19481690.148927242893100
6.25-43.290.16881360.13872756289299

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