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- PDB-1s21: Crystal Structure of AvrPphF ORF2, A Type III Effector from P. sy... -

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Basic information

Entry
Database: PDB / ID: 1s21
TitleCrystal Structure of AvrPphF ORF2, A Type III Effector from P. syringae
ComponentsORF2
KeywordsCHAPERONE / PREDOMINANTLY BETA-STRAND
Function / homologyType III effector HopF2 / AvrPphF-ORF-2 / ORF2
Function and homology information
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2 Å
AuthorsSinger, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.K. / Sondek, J.
CitationJournal: Structure / Year: 2004
Title: Crystal Structures of the Type III Effector Protein AvrPphF and Its Chaperone Reveal Residues Required for Plant Pathogenesis
Authors: Singer, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.K. / Sondek, J.
History
DepositionJan 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF2


Theoretical massNumber of molelcules
Total (without water)22,0501
Polymers22,0501
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.689, 68.334, 88.365
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 ORF2


Mass: 22050.238 Da / Num. of mol.: 1 / Fragment: AvrPphF ORF2 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (bacteria)
Species: Pseudomonas savastanoi / Gene: AvrPphF ORF2 / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL Codon Plus / References: UniProt: Q9K2L5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2962.35
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, sitting drop6.5PEG8000, Bis-Tris, Magnesium Acetate and glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
2912vapor diffusion, sitting drop7.5Ammonium Sulfate, PEG400, HEPES and glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEAug 28, 2002Osmic Confocal "Blue" Optics
RIGAKU RAXIS IV++2IMAGE PLATEAug 26, 2002Osmic Confocal "Blue" Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 16474 / Num. obs: 16442 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1601 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→19.63 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1137637.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 798 4.9 %RANDOM
Rwork0.225 ---
all0.226 16462 --
obs0.225 16408 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1586 Å2 / ksol: 0.358902 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.36 Å20 Å20 Å2
2---2.49 Å20 Å2
3----6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 0 145 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.142.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 116 4.3 %
Rwork0.256 2553 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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