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- PDB-6r8m: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 6r8m
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • NBS-LRR class disease resistance protein Pikh-1
KeywordsPLANT PROTEIN / NLR / Complex / HMA / Rice blast
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 / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...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 / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AVR-Pik protein / NBS-LRR class disease resistance protein
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDe la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004553 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012574 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M02198X United Kingdom
European Research Council743165 United Kingdom
Japan Society for the Promotion of ScienceKAKENHI 15H05779 Japan
Citation
Journal: Elife / Year: 2019
Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor.
Authors: De la Concepcion, J.C. / Franceschetti, M. / MacLean, D. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2019
Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor
Authors: De la Concepcion, J.C. / Franceschetti, M. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 18, 2019Group: Data collection / Refinement description / Category: software / Item: _software.version
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
A: NBS-LRR class disease resistance protein Pikh-1
B: NBS-LRR class disease resistance protein Pikh-1
C: AVR-Pik protein
E: NBS-LRR class disease resistance protein Pikh-1
F: NBS-LRR class disease resistance protein Pikh-1
G: AVR-Pik protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20710
Polymers54,8996
Non-polymers3074
Water5,296294
1
A: NBS-LRR class disease resistance protein Pikh-1
B: NBS-LRR class disease resistance protein Pikh-1
C: AVR-Pik protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6035
Polymers27,4503
Non-polymers1542
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-27 kcal/mol
Surface area11600 Å2
MethodPISA
2
E: NBS-LRR class disease resistance protein Pikh-1
F: NBS-LRR class disease resistance protein Pikh-1
G: AVR-Pik protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6035
Polymers27,4503
Non-polymers1542
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-28 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.456, 80.701, 105.577
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 Pikh-1


Mass: 8388.819 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: Pi-km1, Pikh-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9G5
#2: Protein AVR-Pik protein


Mass: 10672.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8C2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus HT-96 condition A8 [0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5%v/v ...Details: Morpheus HT-96 condition A8 [0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5%v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→29.5 Å / Num. obs: 49337 / % possible obs: 99.8 % / Redundancy: 18.3 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.017 / Rrim(I) all: 0.054 / Net I/σ(I): 31
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.751 / Num. unique obs: 2963 / CC1/2: 0.952 / Rpim(I) all: 0.181 / Rrim(I) all: 0.773 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G10

6g10


Resolution: 1.85→29.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.545 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 2518 5.1 %RANDOM
Rwork0.1864 ---
obs0.1886 46754 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.46 Å2 / Biso mean: 38.435 Å2 / Biso min: 20.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--4.1 Å20 Å2
3----2.2 Å2
Refinement stepCycle: final / Resolution: 1.85→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 18 294 3858
Biso mean--54.7 43.44 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173680
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6344974
X-RAY DIFFRACTIONr_angle_other_deg1.3161.5948553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76422.561164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11615692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711523
X-RAY DIFFRACTIONr_chiral_restr0.070.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
LS refinement shellResolution: 1.848→1.896 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 172 -
Rwork0.291 3374 -
all-3546 -
obs--98.55 %

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