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- PDB-7esw: Root induced Secreted protein Tsp1 from Biocontrol fungi Trichode... -

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Basic information

Entry
Database: PDB / ID: 7esw
TitleRoot induced Secreted protein Tsp1 from Biocontrol fungi Trichoderma virens
ComponentsTrichoderma secreted protein Tsp1
KeywordsSIGNALING PROTEIN / Effector / ellicitor / bio-control agent
Function / homologyeffector-mediated perturbation of host innate immune response by symbiont / extracellular region / Effector TSP1
Function and homology information
Biological speciesHypocrea virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsGupta, G.D.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structure-function analysis reveals Trichoderma virens Tsp1 to be a novel fungal effector protein modulating plant defence.
Authors: Gupta, G.D. / Bansal, R. / Mistry, H. / Pandey, B. / Mukherjee, P.K.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trichoderma secreted protein Tsp1
B: Trichoderma secreted protein Tsp1


Theoretical massNumber of molelcules
Total (without water)29,4152
Polymers29,4152
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-26 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.290, 48.720, 56.200
Angle α, β, γ (deg.)90.000, 112.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Trichoderma secreted protein Tsp1


Mass: 14707.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus)
Strain: Gv29-8 / FGSC 10586 / Gene: TRIVIDRAFT_215947 / Production host: Escherichia coli (E. coli) / References: UniProt: G9MQD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.9M Sodium malonate pH 6.5, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 8, 2018
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→32 Å / Num. obs: 64807 / % possible obs: 99 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 3121 / CC1/2: 0.835 / Rpim(I) all: 0.24 / Rrim(I) all: 0.554

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CWJ

7cwj


Resolution: 1.25→31.95 Å / SU ML: 0.1077 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 16.6264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1745 3215 4.96 %
Rwork0.1508 61573 -
obs0.152 64788 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.13 Å2
Refinement stepCycle: LAST / Resolution: 1.25→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 0 331 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081940
X-RAY DIFFRACTIONf_angle_d1.17032669
X-RAY DIFFRACTIONf_chiral_restr0.0988311
X-RAY DIFFRACTIONf_plane_restr0.0081340
X-RAY DIFFRACTIONf_dihedral_angle_d6.1755266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.22441400.20782568X-RAY DIFFRACTION97.59
1.27-1.290.22331320.19472643X-RAY DIFFRACTION97.54
1.29-1.310.2381410.18742654X-RAY DIFFRACTION97.83
1.31-1.330.25491230.17492632X-RAY DIFFRACTION98.32
1.33-1.360.23941380.16642645X-RAY DIFFRACTION97.55
1.36-1.380.23221260.16782672X-RAY DIFFRACTION98.52
1.38-1.410.19871270.15852638X-RAY DIFFRACTION98.57
1.41-1.440.18281490.15112639X-RAY DIFFRACTION98.31
1.44-1.470.17641380.13732672X-RAY DIFFRACTION98.56
1.47-1.510.17561510.13632659X-RAY DIFFRACTION99.33
1.51-1.550.19331540.12912637X-RAY DIFFRACTION99.04
1.55-1.60.15941220.13622688X-RAY DIFFRACTION99.08
1.6-1.650.16521430.13582686X-RAY DIFFRACTION99.3
1.65-1.710.18731440.1392670X-RAY DIFFRACTION99.43
1.71-1.780.18111330.13352693X-RAY DIFFRACTION99.58
1.78-1.860.17091790.1352660X-RAY DIFFRACTION99.75
1.86-1.960.15341250.13152716X-RAY DIFFRACTION99.68
1.96-2.080.15261490.1292697X-RAY DIFFRACTION99.96
2.08-2.240.15651420.13612720X-RAY DIFFRACTION100
2.24-2.460.15221570.14022687X-RAY DIFFRACTION100
2.46-2.820.16391150.15752766X-RAY DIFFRACTION100
2.82-3.550.18521390.15922734X-RAY DIFFRACTION100
3.55-31.950.17471480.16682797X-RAY DIFFRACTION99.97

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