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- PDB-3zr8: Crystal structure of RxLR effector Avr3a11 from Phytophthora capsici -

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Basic information

Entry
Database: PDB / ID: 3zr8
TitleCrystal structure of RxLR effector Avr3a11 from Phytophthora capsici
ComponentsAVR3A11
KeywordsPROTEIN BINDING / PLANT PATHOGEN INTERACTIONS
Function / homologyArc Repressor Mutant, subunit A - #2460 / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Arc Repressor Mutant, subunit A / Orthogonal Bundle / extracellular region / Mainly Alpha / TRIETHYLENE GLYCOL / RxLR effector protein
Function and homology information
Biological speciesPHYTOPHTHORA CAPSICI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.9 Å
AuthorsBoutemy, L.S. / King, S.R.F. / Win, J. / Hughes, R.K. / Clarke, T.A. / Blumenschein, T.M.A. / Kamoun, S. / Banfield, M.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structures of Phytophthora Rxlr Effector Proteins: A Conserved But Adaptable Fold Underpins Functional Diversity.
Authors: Boutemy, L.S. / King, S.R.F. / Win, J. / Hughes, R.K. / Clarke, T.A. / Blumenschein, T.M.A. / Kamoun, S. / Banfield, M.J.
History
DepositionJun 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: AVR3A11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7134
Polymers7,4921
Non-polymers2213
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.300, 25.330, 90.700
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 AVR3A11


Mass: 7491.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYTOPHTHORA CAPSICI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G1K3S4*PLUS
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENOME CURRENTLY NOT ANNOTATED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.86 % / Description: NONE
Crystal growDetails: 25-30% (W/V) PEG 3350, 0.1 M BIS-TRIS PROPANE PH 6.5-7.0, 0.2 M POTASSIUM THIOCYANATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.73
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73 Å / Relative weight: 1
ReflectionResolution: 0.9→17.41 Å / Num. obs: 34450 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 0.9→17.41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.422 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES AND REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14865 1835 5.1 %RANDOM
Rwork0.1255 ---
obs0.12669 34450 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 0.9→17.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms526 0 12 91 629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022633
X-RAY DIFFRACTIONr_bond_other_d0.0040.02480
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.988856
X-RAY DIFFRACTIONr_angle_other_deg1.03131179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.602584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55223.33327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.038154
X-RAY DIFFRACTIONr_chiral_restr0.0820.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
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_it1.6071.5364
X-RAY DIFFRACTIONr_mcbond_other0.4911.5145
X-RAY DIFFRACTIONr_mcangle_it2.4052594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4853269
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5144.5252
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.34231113
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.9→0.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 143 -
Rwork0.196 2491 -
obs--97.23 %

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