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- PDB-7b1i: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 7b1i
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with the HMA domain of OsHIPP19 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • OSIGBa0128P10.9 protein
KeywordsPLANT PROTEIN / complex / effector / HMA domain / rice / rice blast fungus
Function / homologyHeavy metal-associated isoprenylated plant protein 47 / Avr-Pik / AVR-Pik protein / OSIGBa0128P10.9 protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaidment, J.H.R. / Franceschetti, M. / Banfield, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011216/1 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense.
Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2020
Title: Multiple variants of the blast fungus effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19 with high affinity
Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionNov 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 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
B: OSIGBa0128P10.9 protein
C: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,1942
Polymers19,1942
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-0 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.783, 53.782, 98.026
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 OSIGBa0128P10.9 protein / OsHIPP19 protein / OSIGBa0150F01.4 protein


Mass: 8337.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OSIGBa0150F01.4, OSIGBa0128P10.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01IL6
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 10856.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8, UniProt: A0A219T3Y8*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12M Alcohols [0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol], 0.1M Buffer System 3 pH 8.5 [1M Tris (base); BICINE], ...Details: 0.12M Alcohols [0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol], 0.1M Buffer System 3 pH 8.5 [1M Tris (base); BICINE], 50% v/v Precipitant Mix 1 [40% v/v PEG 500* MME; 20% w/v PEG 20000]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→98.03 Å / Num. obs: 13077 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Net I/σ(I): 12.4 / Num. measured all: 165357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9411.11.12989688110.910.3521.1841.9100
9.11-98.039.60.04715401600.9990.0150.04935.999.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 1.9→98.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.897 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 664 5.1 %RANDOM
Rwork0.1956 ---
obs0.1975 12365 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 max: 82.19 Å2 / Biso mean: 37.001 Å2 / Biso min: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2---0.23 Å20 Å2
3---3.84 Å2
Refinement stepCycle: final / Resolution: 1.9→98.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 67 1275
Biso mean---37.47 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191256
X-RAY DIFFRACTIONr_bond_other_d0.0020.021189
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9541696
X-RAY DIFFRACTIONr_angle_other_deg0.95632774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45624.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08615229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.728157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 45 -
Rwork0.275 889 -
all-934 -
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)
14.26572.3048-1.16486.6342-2.28174.2026-0.08380.30470.3013-0.7010.23720.0232-0.59470.1001-0.15340.3542-0.04490.01070.13920.0090.039444.91810.459107.066
26.09070.26321.61154.78061.47382.04190.0856-0.1673-0.31330.0390.01140.0234-0.0754-0.0004-0.0970.0634-0.00490.00310.00610.00860.019141.2840.129121.548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 76
2X-RAY DIFFRACTION2C33 - 113

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