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- PDB-7a8w: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 7a8w
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
Components
  • NBS-LRR class disease resistance protein
  • Uncharacterized protein
KeywordsANTIFUNGAL PROTEIN / Fungal effector / HMA domain / NLR protein / MAX effector
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NBS-LRR class disease resistance protein / AVR-Pik protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMaidment, J.H.R. / De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M02198X United Kingdom
European Research Council (ERC)743165 United Kingdom
John Innes FoundationRotation Programme United Kingdom
CitationJournal: Plos Pathog. / Year: 2021
Title: The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface.
Authors: De la Concepcion, J.C. / Maidment, J.H.R. / Longya, A. / Xiao, G. / Franceschetti, M. / Banfield, M.J.
History
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: NBS-LRR class disease resistance protein
BBB: NBS-LRR class disease resistance protein
CCC: Uncharacterized protein
DDD: NBS-LRR class disease resistance protein
EEE: NBS-LRR class disease resistance protein
FFF: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)56,1836
Polymers56,1836
Non-polymers00
Water1,40578
1
AAA: NBS-LRR class disease resistance protein
BBB: NBS-LRR class disease resistance protein
CCC: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,0923
Polymers28,0923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
DDD: NBS-LRR class disease resistance protein
EEE: NBS-LRR class disease resistance protein
FFF: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,0923
Polymers28,0923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.784, 80.205, 105.683
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
NBS-LRR class disease resistance protein / NBS-LRR class disease resistance protein Pikh-1


Mass: 8622.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pi-km1, Pikh-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9G5
#2: Protein Uncharacterized protein


Mass: 10847.306 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus)
Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_15972 / Production host: Escherichia coli (E. coli) / References: UniProt: G4MXW3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; ...Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5% v/v Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→46.17 Å / Num. obs: 31604 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Net I/σ(I): 23.9
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2694 / CC1/2: 0.925 / Rpim(I) all: 0.278 / Rrim(I) all: 1.034 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata processing
Aimless0.6.1data scaling
PHASER2.7.17phasing
REFMAC5.8.0266refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 2.15→44.165 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.997 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2722 1510 4.786 %
Rwork0.2241 30038 -
all0.227 --
obs-31548 99.921 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.54 Å2
Baniso -1Baniso -2Baniso -3
1--4.396 Å2-0 Å20 Å2
2--7.349 Å2-0 Å2
3----2.953 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 0 78 3521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173563
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.6294716
X-RAY DIFFRACTIONr_angle_other_deg1.1831.5998223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04722.756156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84715669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7231521
X-RAY DIFFRACTIONr_chiral_restr0.0560.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined0.1980.2612
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23237
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21651
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.212
X-RAY DIFFRACTIONr_nbd_other0.210.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.23
X-RAY DIFFRACTIONr_mcbond_it4.6316.0481794
X-RAY DIFFRACTIONr_mcbond_other4.6236.0471793
X-RAY DIFFRACTIONr_mcangle_it6.2919.0382226
X-RAY DIFFRACTIONr_mcangle_other6.2919.0392227
X-RAY DIFFRACTIONr_scbond_it5.1176.5641713
X-RAY DIFFRACTIONr_scbond_other5.1146.5631713
X-RAY DIFFRACTIONr_scangle_it7.3049.6182488
X-RAY DIFFRACTIONr_scangle_other7.2949.6172488
X-RAY DIFFRACTIONr_lrange_it9.14669.8053669
X-RAY DIFFRACTIONr_lrange_other9.14869.7883662

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