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- PDB-9eyl: dN53 deletion variant of monomeric Fav - actinoporin from Orbicel... -

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Basic information

Entry
Database: PDB / ID: 9eyl
TitledN53 deletion variant of monomeric Fav - actinoporin from Orbicella faveolata
ComponentsdN53_Fav
KeywordsTOXIN / Actinoporin / Pore-forming toxin / Orbicella faveolata
Function / homologyTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
Function and homology information
Biological speciesOrbicella faveolata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSolinc, G. / Svigelj, T. / Anderluh, G. / Podobnik, M.
Funding support Slovenia, United Kingdom, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyJ4-8225 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
Other private United Kingdom
CitationJournal: To Be Published
Title: dN53 deletion variant of monomeric Fav - actinoporin from Orbicella faveolata
Authors: Solinc, G. / Anderluh, G. / Podobnik, M.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dN53_Fav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3174
Polymers23,0031
Non-polymers3143
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-16 kcal/mol
Surface area8170 Å2
Unit cell
Length a, b, c (Å)61.011, 61.011, 91.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-621-

HOH

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Components

#1: Protein dN53_Fav


Mass: 23002.561 Da / Num. of mol.: 1 / Mutation: dN53
Source method: isolated from a genetically manipulated source
Details: This protein was expressed with an N-terminal deletion of 53 residues compared to the wild type. The deletion construct has three additional residues at the N-terminal (GHM) from the expression system.
Source: (gene. exp.) Orbicella faveolata (invertebrata) / Plasmid: pET28a (+)
Details (production host): modified pET28a (+) plasmid with the N-terminal 6-histidine tag and TEV restriction site ENLYFQGHM
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.14 Å3/Da / Density % sol: 42.65 % / Description: hexagonal rods
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Li2SO4 / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→45.8 Å / Num. obs: 32274 / % possible obs: 99.95 % / Redundancy: 10.4 % / Biso Wilson estimate: 11.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09948 / Rpim(I) all: 0.03232 / Rrim(I) all: 0.1047 / Net I/σ(I): 18.73
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.7893 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 3195 / CC1/2: 0.887 / CC star: 0.969 / Rpim(I) all: 0.26 / Rrim(I) all: 0.8317 / % possible all: 99.59

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDS0.76data reduction
XDS0.76data scaling
PHASER(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.8 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 1978 6.13 %
Rwork0.1602 --
obs0.1617 32269 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 18 274 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071550
X-RAY DIFFRACTIONf_angle_d0.8862124
X-RAY DIFFRACTIONf_dihedral_angle_d6.905223
X-RAY DIFFRACTIONf_chiral_restr0.059223
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.32811380.23132141X-RAY DIFFRACTION99
1.54-1.580.22171350.19582125X-RAY DIFFRACTION100
1.58-1.630.22561400.18262133X-RAY DIFFRACTION100
1.63-1.680.22811390.16982135X-RAY DIFFRACTION100
1.68-1.740.19031430.17632142X-RAY DIFFRACTION100
1.74-1.810.21141380.16782118X-RAY DIFFRACTION100
1.81-1.890.20031360.17512162X-RAY DIFFRACTION100
1.89-1.990.19461400.15572139X-RAY DIFFRACTION100
1.99-2.110.17861390.1522165X-RAY DIFFRACTION100
2.11-2.280.15241410.15562147X-RAY DIFFRACTION100
2.28-2.510.19311430.16722176X-RAY DIFFRACTION100
2.51-2.870.17871440.16022186X-RAY DIFFRACTION100
2.87-3.610.15911450.14822201X-RAY DIFFRACTION100
3.62-45.80.16941570.14342321X-RAY DIFFRACTION100

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