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- PDB-5a6w: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 5a6w
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp1 from rice (Oryza sativa)
Components
  • AVR-PIK PROTEIN
  • RESISTANCE PROTEIN PIKP-1
KeywordsANTIVIRAL PROTEIN / RICE BLAST DISEASE / PLANT DISEASE RESISTANCE / EFFECTOR PROTEIN / INTEGRATED HMA DOMAIN
Function / homology
Function and homology information


defense response to other organism / ADP binding / metal ion binding
Similarity search - Function
: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA ...: / AVR-Pik-like, HMA interaction domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / : / Leucine-rich repeat region / 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 / Resistance protein Pikp-1
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
MAGNAPORTHE ORYZAE (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMaqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
CitationJournal: Elife / Year: 2015
Title: Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
Authors: Maqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionJul 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RESISTANCE PROTEIN PIKP-1
B: RESISTANCE PROTEIN PIKP-1
C: AVR-PIK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8048
Polymers26,4603
Non-polymers3445
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-13.1 kcal/mol
Surface area13810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.410, 118.410, 35.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RESISTANCE PROTEIN PIKP-1


Mass: 7816.232 Da / Num. of mol.: 2 / Fragment: PIKP-HMA, UNP RESIDUES 186-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Strain: K60 / Plasmid: POPINS3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SHUFFLE / References: UniProt: E9KPB5
#2: Protein AVR-PIK PROTEIN


Mass: 10827.340 Da / Num. of mol.: 1 / Fragment: AVR-PIKD, UNP RESIDUES 22-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNAPORTHE ORYZAE (rice blast fungus) / Strain: SASA2 / Plasmid: POPINA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SHUFFLE / References: UniProt: C4B8B8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 2M AMMONIUM SULPHATE, 0.1M CHES PH 9 AND 20% PEG335

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→39.47 Å / Num. obs: 32549 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 17.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A6P

5a6p


Resolution: 1.6→39.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.627 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20544 1712 5 %RANDOM
Rwork0.17763 ---
obs0.17908 32549 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 21 138 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191809
X-RAY DIFFRACTIONr_bond_other_d0.0010.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9872433
X-RAY DIFFRACTIONr_angle_other_deg0.72934228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8345230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92924.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6291512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
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_it1.6342.106914
X-RAY DIFFRACTIONr_mcbond_other1.6182.103913
X-RAY DIFFRACTIONr_mcangle_it2.6313.1341137
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.252.404895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 124 -
Rwork0.196 2379 -
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)
14.15360.7948-1.00991.8979-0.85651.7210.0140.2885-0.30960.018-0.049-0.37950.0303-0.09570.0350.0341-0.04870.02150.0964-0.03760.132-16.5550.9932-9.9001
21.31680.2792-0.19941.67350.58471.7269-0.0092-0.0722-0.26870.09760.1146-0.23950.07380.1242-0.10540.01170.0047-0.01190.0630.00180.0799-31.6302-6.8926-0.515
31.05520.0192-0.10150.54180.3921.3285-0.03060.00790.0321-0.0227-0.0130.02-0.0710.00080.04350.04620.0008-0.01090.0284-0.00310.0043-43.03956.93484.9588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 258
2X-RAY DIFFRACTION2B184 - 258
3X-RAY DIFFRACTION3C31 - 113

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