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- PDB-7nlj: Complex of rice blast (Magnaporthe oryzae) effector protein APikL... -

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Basic information

Entry
Database: PDB / ID: 7nlj
TitleComplex of rice blast (Magnaporthe oryzae) effector protein APikL2A with host target sHMA25 from Setaria italica
Components
  • APikL2A
  • sHMA25
KeywordsPLANT PROTEIN / complex / heavy-metal associated domain / fungal virulence protein
Function / homologyHeavy metal-associated isoprenylated plant protein 16/46/47 / Uncharacterized protein
Function and homology information
Biological speciesSetaria italica (foxtail millet)
Pyricularia oryzae Y34 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBentham, A.R. / Banfield, M.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)743165 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
CitationJournal: Plos Pathog. / Year: 2021
Title: A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum.
Authors: Bentham, A.R. / Petit-Houdenot, Y. / Win, J. / Chuma, I. / Terauchi, R. / Banfield, M.J. / Kamoun, S. / Langner, T.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sHMA25
B: APikL2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2865
Polymers19,1002
Non-polymers1863
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint9 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.208, 46.684, 88.953
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 sHMA25


Mass: 8352.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Setaria italica (foxtail millet) / Gene: 101766303, SETIT_7G131400v2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle / References: UniProt: K3YAU1
#2: Protein APikL2A


Mass: 10747.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae Y34 (fungus) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus well H10 Molecular Dimensions. 0.1 M Amino acids, 0.1 M Buffer System 3, 50% v/v Precipitant Mix 2

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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: 1.8→41.039 Å / Num. obs: 18505 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.99 / Rrim(I) all: 0.058 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.7 % / Num. unique obs: 1060 / CC1/2: 0.798 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6w

5a6w


Resolution: 1.8→41.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.503 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 813 4.4 %RANDOM
Rwork0.1991 ---
obs0.2012 17641 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 max: 109.4 Å2 / Biso mean: 44.666 Å2 / Biso min: 26.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0 Å2
2---1.04 Å20 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 1.8→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 12 83 1416
Biso mean--51.99 45.59 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131370
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171357
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6361842
X-RAY DIFFRACTIONr_angle_other_deg1.3841.5943124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70521.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.162159
X-RAY DIFFRACTIONr_chiral_restr0.070.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 66 -
Rwork0.276 1274 -
all-1340 -
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)
14.4986-0.38121.39263.28350.37152.82550.03790.41860.258-0.17190.014-0.2712-0.11960.4886-0.05190.0389-0.0150.00520.0930.00590.045913.285417.7487-14.8976
23.79360.58430.60392.78121.17054.00930.3041-0.4276-0.5090.2201-0.20180.05380.5216-0.4024-0.10230.0824-0.0755-0.04090.07760.05670.0764-1.8526.599-9.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2B23 - 113

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