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- PDB-8r7d: Complex of rice blast (Magnaporthe oryzae) mutant effector protei... -

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Basic information

Entry
Database: PDB / ID: 8r7d
TitleComplex of rice blast (Magnaporthe oryzae) mutant effector protein PWL2-SNDE with the HMA domain of OsHIPP43 from rice (Oryza sativa)
Components
  • Os01g0507700 protein
  • Pwl2 protein
KeywordsPLANT PROTEIN / Pathogen effector / host target protein / rice blast / disease resistance
Function / homologyHeavy metal binding protein HIPP/ATX1-like / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / response to stimulus / metal ion binding / Pwl2 protein / Os01g0507700 protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Pyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZdrzalek, R. / Banfield, M.J.
Funding support United Kingdom, European Union, Japan, 14items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W00108X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/WW002221/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V016342 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V015508/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9795 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9796 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X010996/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
European Research Council (ERC)743165European Union
Japan Society for the Promotion of Science (JSPS)20H05681 Japan
Gatsby Charitable Foundation United Kingdom
John Innes Foundation United Kingdom
CitationJournal: To Be Published
Title: Bioengineering a plant NLR immune receptor with a robust recognition interface towards a conserved fungal pathogen effector
Authors: Zdrzalek, R. / Xi, Y. / Langner, T. / Bentham, A.R. / Petit-Houdenot, Y. / Harant, A. / Shimizu, M. / Were, V. / Talbot, N.J. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Os01g0507700 protein
B: Pwl2 protein
C: Os01g0507700 protein
D: Pwl2 protein


Theoretical massNumber of molelcules
Total (without water)66,0794
Polymers66,0794
Non-polymers00
Water77543
1
A: Os01g0507700 protein
B: Pwl2 protein


Theoretical massNumber of molelcules
Total (without water)33,0392
Polymers33,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-3 kcal/mol
Surface area8960 Å2
MethodPISA
2
C: Os01g0507700 protein
D: Pwl2 protein


Theoretical massNumber of molelcules
Total (without water)33,0392
Polymers33,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-2 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.378, 66.804, 81.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Os01g0507700 protein


Mass: 16658.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: Os01g0507700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LJL3
#2: Protein Pwl2 protein


Mass: 16380.946 Da / Num. of mol.: 2 / Mutation: S42R, N52R, D62R, E89R,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: MGG_04301 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EI71
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→47.13 Å / Num. obs: 13157 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.08 / Rrim(I) all: 0.296 / Χ2: 0.95 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 1.351 / Num. measured all: 20237 / Num. unique obs: 1454 / CC1/2: 0.765 / Rpim(I) all: 0.374 / Rrim(I) all: 1.402 / Χ2: 0.95 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.13 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.848 / SU B: 25.106 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 1.034 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28582 741 5.6 %RANDOM
Rwork0.21559 ---
obs0.21971 12376 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.982 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å2-0 Å2
2--1.52 Å2-0 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 0 43 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162652
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.8613932
X-RAY DIFFRACTIONr_angle_other_deg0.5921.816110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0435361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.016536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75410483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7592.2471441
X-RAY DIFFRACTIONr_mcbond_other1.7562.2471441
X-RAY DIFFRACTIONr_mcangle_it2.8154.0271797
X-RAY DIFFRACTIONr_mcangle_other2.8144.0281798
X-RAY DIFFRACTIONr_scbond_it2.6382.6331482
X-RAY DIFFRACTIONr_scbond_other2.6292.6311481
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2224.692134
X-RAY DIFFRACTIONr_long_range_B_refined5.86822.863167
X-RAY DIFFRACTIONr_long_range_B_other5.85922.853167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 27 -
Rwork0.27 944 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8087-0.6809-1.5493.86670.97018.5325-0.102-0.22990.69230.0742-0.00350.1357-0.5363-0.22940.10550.04530.0238-0.01910.0197-0.04160.1785-2.1223.25914.87
24.04811.58991.04663.19181.90834.142-0.13220.08610.3201-0.34440.1475-0.1557-0.21660.2601-0.01530.0404-0.01650.02890.0207-0.00150.10817.51520.11310.062
34.2141-0.6175-1.35792.946-0.78448.43680.02780.16340.4894-0.4545-0.0080.3003-0.3375-0.235-0.01970.10390.0069-0.06650.01410.00760.129625.96152.1326.756
42.66121.03040.75384.77160.86813.0084-0.0117-0.2054-0.0522-0.219-0.04040.05730.2743-0.18070.05210.0482-0.01150.01370.02680.01510.040529.26342.08310.786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 94
2X-RAY DIFFRACTION2B23 - 132
3X-RAY DIFFRACTION3C26 - 94
4X-RAY DIFFRACTION4D23 - 133

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