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- PDB-3zrg: Crystal structure of RxLR effector PexRD2 from Phytophthora infestans -

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Basic information

Entry
Database: PDB / ID: 3zrg
TitleCrystal structure of RxLR effector PexRD2 from Phytophthora infestans
ComponentsPEXRD2 FAMILY SECRETED RXLR EFFECTOR PEPTIDE, PUTATIVE
KeywordsPROTEIN BINDING / PLANT PATHOGEN INTERACTIONS
Function / homology
Function and homology information


host cell cytoplasm / host cell nucleus / extracellular region
Similarity search - Function
Arc Repressor Mutant, subunit A - #2470 / PexRD2, WYL domain / WYL domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / PexRD2 family secreted RxLR effector peptide, putative / RxLR effector protein PexRD2
Similarity search - Component
Biological speciesPHYTOPHTHORA INFESTANS (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKing, S.R.F. / Boutemy, L.S. / 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: PEXRD2 FAMILY SECRETED RXLR EFFECTOR PEPTIDE, PUTATIVE
B: PEXRD2 FAMILY SECRETED RXLR EFFECTOR PEPTIDE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2719
Polymers14,7112
Non-polymers5597
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-16.8 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.450, 52.920, 53.730
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 PEXRD2 FAMILY SECRETED RXLR EFFECTOR PEPTIDE, PUTATIVE / PEXRD2


Mass: 7355.747 Da / Num. of mol.: 2 / Fragment: EFFECTOR DOMAIN, RESIDUES 57-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYTOPHTHORA INFESTANS (potato late blight agent)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0NIL2, UniProt: D0NIN5*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL TWO RESIDUES ARE NON-NATIVE, AND DERIVED FROM THE PROTEASE CLEAVAGE SITE FOLLOWING ...N-TERMINAL TWO RESIDUES ARE NON-NATIVE, AND DERIVED FROM THE PROTEASE CLEAVAGE SITE FOLLOWING REMOVAL OF AFFINITY- TAG

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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: 2.14 Å3/Da / Density % sol: 42.43 % / Description: NONE
Crystal growpH: 7.5
Details: 2.6 M AMMONIUM SULPHATE, 0.1 M TRIS.HCL PH 7.5 AND 0.2 M AMMONIUM BROMIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→37.7 Å / Num. obs: 12601 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 9.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→37.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.049 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 656 4.9 %RANDOM
Rwork0.18937 ---
obs0.19204 12601 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 7 127 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221039
X-RAY DIFFRACTIONr_bond_other_d0.0020.02722
X-RAY DIFFRACTIONr_angle_refined_deg1.44721412
X-RAY DIFFRACTIONr_angle_other_deg0.97631780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2055149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30724.83931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79215212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
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_it0.761.5682
X-RAY DIFFRACTIONr_mcbond_other0.2811.5275
X-RAY DIFFRACTIONr_mcangle_it1.29221092
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6293357
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1314.5309
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 49 -
Rwork0.239 904 -
obs--99.58 %
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)
12.4231-1.35540.92214.1478-1.1672.02830.0005-0.0427-0.11940.04380.09720.26870.0397-0.1375-0.09770.0038-0.00860.01250.0372-0.00090.017810.7104-8.003421.8877
23.3375-0.4951-1.60852.27010.21133.32630.0381-0.04880.18840.0166-0.0416-0.0594-0.1784-0.00870.00350.059-0.0061-0.01630.03660.02420.037118.37142.57118.8855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 120
2X-RAY DIFFRACTION2B55 - 119

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