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

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Basic information

Entry
Database: PDB / ID: 7cwp
TitleRoot induced Secreted protein Tsp1 from Biocontrol fungi Trichoderma virens
ComponentsRoot induced signalling protein
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: 2.1 Å
AuthorsGupta, G.D.
CitationJournal: To Be Published
Title: Crystal structure of root induced Secreted protein Tsp1 from Biocontrol fungi Trichoderma virens
Authors: Gupta, G.D.
History
DepositionAug 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Root induced signalling protein
B: Root induced signalling protein
C: Root induced signalling protein
D: Root induced signalling protein


Theoretical massNumber of molelcules
Total (without water)58,8304
Polymers58,8304
Non-polymers00
Water8,593477
1
A: Root induced signalling protein

B: Root induced signalling protein


Theoretical massNumber of molelcules
Total (without water)29,4152
Polymers29,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3160 Å2
ΔGint-26 kcal/mol
Surface area10770 Å2
MethodPISA
2
C: Root induced signalling protein
D: Root induced signalling protein


Theoretical massNumber of molelcules
Total (without water)29,4152
Polymers29,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-30 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 66.700, 168.000
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 signalling protein


Mass: 14707.418 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) / References: UniProt: G9MQD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9 M sodium malonate pH 6.5, 5 mM glucose, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→42.89 Å / Num. obs: 29074 / % possible obs: 95.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.03 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.055 / Rrim(I) all: 0.129 / Net I/σ(I): 9.4 / Num. measured all: 131390
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.164.40.4841073024130.8790.2340.5413.197.1
8.91-42.894.20.04717114040.9960.0250.05419.687.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.994 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1465 5.05 %
Rwork0.176 27537 -
obs0.1785 29002 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.32 Å2 / Biso mean: 22.605 Å2 / Biso min: 10.24 Å2
Refinement stepCycle: final / Resolution: 2.1→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 0 477 4265
Biso mean---27.73 -
Num. residues----511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053904
X-RAY DIFFRACTIONf_angle_d0.7655370
X-RAY DIFFRACTIONf_chiral_restr0.049620
X-RAY DIFFRACTIONf_plane_restr0.005685
X-RAY DIFFRACTIONf_dihedral_angle_d8.0982274
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.1750.27641200.2127280597
2.175-2.26190.28781450.1893275797
2.2619-2.36470.21691640.1845274898
2.3647-2.48920.25441450.1921276697
2.4892-2.64480.24121430.2015276796
2.6448-2.84850.27531570.1882272995
2.8485-3.13420.23291360.1866276296
3.1342-3.58540.19761420.1613271393
3.5854-4.50870.20091470.1452273492
4.5087-19.9940.19511660.1699275690

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