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- PDB-9fei: Crystal structure of protein D: defoliating toxin form Fusarium o... -

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Basic information

Entry
Database: PDB / ID: 9fei
TitleCrystal structure of protein D: defoliating toxin form Fusarium oxysporum f.sp. vasinfectum
ComponentsDefoliating protein: protein D
KeywordsTOXIN / defoliating / plant / pathogens / fungi
Function / homology:
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsTroilo, F. / Doddi, A. / Faino, L. / Bonaccorsi Di Patti, M.C. / Di Matteo, A. / Giardina, G.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
Other governmentRM12117A5BDD4AEC
European Union (EU)IR0000009European Union
CitationJournal: To Be Published
Title: Crystal structure of FovDEF: defoliating toxin form Fusarium oxysporum f.sp. vasinfectum
Authors: Troilo, F. / Doddi, A. / Faino, L. / Bonaccorsi Di Patti, M.C. / Di Matteo, A. / Giardina, G.
History
DepositionMay 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defoliating protein: protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5155
Polymers26,6751
Non-polymers8404
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-71 kcal/mol
Surface area9840 Å2
Unit cell
Length a, b, c (Å)27.843, 50.031, 72.277
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Defoliating protein: protein D


Mass: 26674.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH=7.5 1.4 M sodium citrate Tribasic Dihydrate Protein concentration= 7. 6mg/ml Soaking with HgCl2 over night

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2022
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 1.47→71.4 Å / Num. obs: 33146 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.5
Reflection shellResolution: 1.475→1.5 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1619 / CC1/2: 0.775 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimless0.7.7data scaling
XDSBUILT 20220110data reduction
CRANK22.0.315phasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→71.4 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.119 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18771 1648 5 %RANDOM
Rwork0.16135 ---
obs0.16269 31498 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.66 Å2
2---0.44 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.47→71.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 18 184 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121529
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161471
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6372078
X-RAY DIFFRACTIONr_angle_other_deg0.571.5723399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.77555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74810267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3392.118745
X-RAY DIFFRACTIONr_mcbond_other2.3342.116745
X-RAY DIFFRACTIONr_mcangle_it3.2853.784928
X-RAY DIFFRACTIONr_mcangle_other3.3053.786929
X-RAY DIFFRACTIONr_scbond_it4.5982.653784
X-RAY DIFFRACTIONr_scbond_other4.5872.654782
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8224.6091147
X-RAY DIFFRACTIONr_long_range_B_refined8.15228.371733
X-RAY DIFFRACTIONr_long_range_B_other7.99626.031682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.475→1.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 105 -
Rwork0.259 2306 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.79 Å / Origin y: 0.1495 Å / Origin z: 16.6998 Å
111213212223313233
T0.0082 Å2-0.0021 Å2-0.001 Å2-0.022 Å20.0056 Å2--0.0041 Å2
L0.0833 °2-0.1373 °2-0.0782 °2-0.3132 °20.0414 °2--0.1649 °2
S0.019 Å °0.0043 Å °0.0079 Å °-0.0473 Å °-0.0029 Å °-0.0067 Å °-0.0008 Å °-0.0168 Å °-0.0161 Å °

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