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- PDB-7p22: Thaumatin-like protein of Amycolatopsis rifamycinica -

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Basic information

Entry
Database: PDB / ID: 7p22
TitleThaumatin-like protein of Amycolatopsis rifamycinica
ComponentsThaumatin pathogenesis-like protein
KeywordsUNKNOWN FUNCTION / Thaumatin-like protein
Function / homologyThaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Thaumatin pathogenesis-like protein
Function and homology information
Biological speciesAmycolatopsis rifamycinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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. / Keller, W. / Hofer, G. / Odabas, M.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin pathogenesis-like protein
B: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)52,1292
Polymers52,1292
Non-polymers00
Water6,846380
1
A: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)26,0651
Polymers26,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thaumatin pathogenesis-like protein


Theoretical massNumber of molelcules
Total (without water)26,0651
Polymers26,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.341, 80.341, 169.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin pathogenesis-like protein


Mass: 26064.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis rifamycinica (bacteria) / Gene: DV20_29330 / Plasmid: pJC40 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY / References: UniProt: A0A066TYR3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: JCSG+ D1 condition (0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.0 and 30 % v/v PEG 400)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.87→46.29 Å / Num. obs: 46839 / % possible obs: 99.92 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1317 / Rpim(I) all: 0.05489 / Rrim(I) all: 0.143 / Net I/σ(I): 11.35
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.127 / Num. unique obs: 4587 / CC1/2: 0.648 / Rpim(I) all: 0.4667 / % possible all: 99.91

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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: 1.87→46.29 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2396 5.09 %
Rwork0.1815 44663 -
obs0.1828 46839 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.05 Å2 / Biso mean: 27.611 Å2 / Biso min: 14.88 Å2
Refinement stepCycle: final / Resolution: 1.87→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 0 380 3648
Biso mean---34.73 -
Num. residues----441
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-1.90.28011260.2665250797
1.9-1.940.26711240.24932585100
1.94-1.990.23921350.23252574100
1.99-2.040.25941430.22442605100
2.04-2.10.27981610.21122551100
2.1-2.160.21041270.19912611100
2.16-2.230.23671070.19652638100
2.23-2.310.23151330.19652601100
2.31-2.40.22941390.18572616100
2.4-2.510.24531380.18752620100
2.51-2.640.23331410.18282607100
2.64-2.80.21521500.19142626100
2.81-3.020.23341610.18762618100
3.02-3.330.21241360.17752663100
3.33-3.810.17651580.15732668100
3.81-4.80.13791460.15112713100
4.8-46.290.19941710.16952860100

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