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

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Basic information

Entry
Database: PDB / ID: 7cwj
TitleRoot induced Secreted protein Tsp1 from Biocontrol fungi Trichoderma virens
ComponentsRoot induced effector 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 / SAD / Resolution: 1.61 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
DepositionAug 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Root induced effector protein Tsp1
B: Root induced effector protein Tsp1
C: Root induced effector protein Tsp1
D: Root induced effector protein Tsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7618
Polymers59,3924
Non-polymers3684
Water11,277626
1
A: Root induced effector protein Tsp1
hetero molecules

B: Root induced effector protein Tsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9725
Polymers29,6962
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4130 Å2
ΔGint-31 kcal/mol
Surface area11380 Å2
MethodPISA
2
C: Root induced effector protein Tsp1
D: Root induced effector protein Tsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7883
Polymers29,6962
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.658, 67.478, 170.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Root induced effector protein Tsp1


Mass: 14848.104 Da / Num. of mol.: 4
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) / Variant (production host): Rosetta (DE3) / References: UniProt: G9MQD3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.9 M 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: 0.9788 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.6→44.1 Å / Num. obs: 67496 / % possible obs: 96.2 % / Redundancy: 12.1 % / Biso Wilson estimate: 17.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Net I/σ(I): 27.5 / Num. measured all: 818842 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.636.80.4163.525100.8570.1690.45173.2
8.77-44.110.70.0425230.9990.0130.04499.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
Aimless0.5.21data scaling
RESOLVEphasing
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.61→23.952 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.5 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1995 3377 5.07 %
Rwork0.1507 63252 -
obs0.1532 66629 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.42 Å2 / Biso mean: 23.802 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 1.61→23.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 56 626 4514
Biso mean--35.33 31.98 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014007
X-RAY DIFFRACTIONf_angle_d1.0885517
X-RAY DIFFRACTIONf_chiral_restr0.066633
X-RAY DIFFRACTIONf_plane_restr0.007700
X-RAY DIFFRACTIONf_dihedral_angle_d8.5842360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.6330.26921040.167206376
1.633-1.65740.25521160.1644210580
1.6574-1.68330.25551270.1653226884
1.6833-1.71090.25031280.164235088
1.7109-1.74040.23551300.1625251393
1.7404-1.7720.24551540.1566260296
1.772-1.80610.24661500.1575266199
1.8061-1.84290.22221510.15762687100
1.8429-1.8830.2241590.15442672100
1.883-1.92680.24991460.15262728100
1.9268-1.97490.22091440.14052698100
1.9749-2.02830.19781210.14522725100
2.0283-2.08790.20161370.14232736100
2.0879-2.15530.19221190.14222745100
2.1553-2.23230.20751340.14572703100
2.2323-2.32160.20631490.14392744100
2.3216-2.42710.1791510.14592726100
2.4271-2.5550.20811590.15692725100
2.555-2.71480.20571260.16852772100
2.7148-2.92410.23281570.16412726100
2.9241-3.21770.16911430.15852779100
3.2177-3.68190.18521420.13652789100
3.6819-4.63330.14891590.12622813100
4.6333-23.950.19721710.1688292299

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