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- PDB-6r5j: New MAX Effector from Magnaporthe oryzae -

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Basic information

Entry
Database: PDB / ID: 6r5j
TitleNew MAX Effector from Magnaporthe oryzae
ComponentsUncharacterized protein
KeywordsIMMUNOSUPPRESSANT / Max effector NMR
Function / homologyToxB-like N-terminal, ascomycota / ToxB N-terminal domain / ToxB-like N-terminal ascomycota domain-containing protein
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsHoh, F. / Padilla, A. / De Guillen, K.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE20-0016 France
CitationJournal: To Be Published
Title: New MAX Effector from Magnaporthe oryzae
Authors: Hoh, F. / Padilla, A. / De Guillen, K.
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3523
Polymers14,0692
Non-polymers2821
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: AU
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint3 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.341, 24.760, 68.613
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 7034.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain P131) (fungus)
Strain: P131 / Gene: OOW_P131scaffold00585g1 / Production host: Escherichia coli (E. coli) / References: UniProt: L7J9X7
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0,1M Hepes pH 7.5 1.6M Ammonium Sulfate 1,6M PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→34.59 Å / Num. obs: 59102 / % possible obs: 93.7 % / Redundancy: 2.5 % / Net I/σ(I): 14
Reflection shellResolution: 1.38→1.43 Å / Num. unique obs: 2877

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NMR model

Resolution: 1.38→34.589 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.59
RfactorNum. reflection% reflection
Rfree0.1705 1189 5.05 %
Rwork0.1427 --
obs0.1442 23545 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.33 Å2 / Biso mean: 15.0328 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.38→34.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 19 120 1109
Biso mean--35.56 27.3 -
Num. residues----135
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3801-1.44290.18961050.1348213172
1.4429-1.51890.20391430.1228267090
1.5189-1.61410.18271430.1222289796
1.6141-1.73870.20231430.1267293198
1.7387-1.91370.15961700.1328289997
1.9137-2.19060.17071650.1314289597
2.1906-2.75970.1541640.1483291996
2.7597-100.16991560.15301497

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