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- PDB-7p23: Thaumatin-like protein of Puccinia graminis -

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Basic information

Entry
Database: PDB / ID: 7p23
TitleThaumatin-like protein of Puccinia graminis
ComponentsThaumatin-like protein of Puccinia graminis
KeywordsUNKNOWN FUNCTION / Thaumatin-like protein
Function / homologyThaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / defense response / Thaumatin-like protein 1
Function and homology information
Biological speciesPuccinia graminis f. sp. tritici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEder, M. / Hofer, G. / Odabas, M. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundF 4604-B19 Austria
CitationJournal: To Be Published
Title: The structure of Thaumatin-like proteins of a bacterial, a fungal and an animal origin
Authors: Eder, M. / Hofer, G. / Odabas, M. / Keller, W.
History
DepositionJul 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: 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: Thaumatin-like protein of Puccinia graminis
B: Thaumatin-like protein of Puccinia graminis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0333
Polymers52,0102
Non-polymers231
Water11,259625
1
A: Thaumatin-like protein of Puccinia graminis


Theoretical massNumber of molelcules
Total (without water)26,0051
Polymers26,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thaumatin-like protein of Puccinia graminis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0282
Polymers26,0051
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.140, 77.523, 143.896
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 Thaumatin-like protein of Puccinia graminis


Mass: 26004.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia graminis f. sp. tritici (strain CRL 75-36-700-3 / race SCCL) (fungus)
Strain: CRL 75-36-700-3 / race SCCL / Gene: PGTG_18309 / Plasmid: pPpT4-alpha / Production host: Komagataella pastoris (fungus) / Strain (production host): CBS7435 / References: UniProt: E3L7F9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: PACT premier F12 (0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, and 20 % w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→42.2 Å / Num. obs: 79992 / % possible obs: 99.96 % / Redundancy: 12.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1396 / Rpim(I) all: 0.04067 / Rrim(I) all: 0.1456 / Net I/σ(I): 10.34
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.298 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 7882 / CC1/2: 0.703 / Rpim(I) all: 0.3669 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ahn

2ahn


Resolution: 1.5→42.2 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 1099 1.37 %
Rwork0.1434 78920 -
obs0.144 79992 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.13 Å2 / Biso mean: 26.2133 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.5→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 1 625 4162
Biso mean--46.52 41.66 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.570.23821340.20189709984399
1.57-1.650.24821360.158197369872100
1.65-1.750.19211360.135497679903100
1.75-1.890.2071360.131497649900100
1.89-2.080.18971370.122498229959100
2.08-2.380.17341370.131398539990100
2.38-30.18671390.1578997510114100
3-42.20.18191440.14291029410438100

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