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- PDB-8txf: AvrB bound with RIN4 C-NOI motif -

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Basic information

Entry
Database: PDB / ID: 8txf
TitleAvrB bound with RIN4 C-NOI motif
Components
  • Avirulence protein B
  • RIN4
KeywordsTRANSFERASE / Protein complex
Function / homologyAvirulence B/C / Avirulence B/C superfamily / : / Avirulence protein / extracellular region / Avirulence protein B
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsPeng, W. / Orth, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134945 United States
CitationJournal: Sci Adv / Year: 2024
Title: Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4.
Authors: Peng, W. / Garcia, N. / Servage, K.A. / Kohler, J.J. / Ready, J.M. / Tomchick, D.R. / Fernandez, J. / Orth, K.
History
DepositionAug 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avirulence protein B
B: RIN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,62016
Polymers39,6912
Non-polymers92914
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint29 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.796, 119.903, 46.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1105-

HOH

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Components

#1: Protein Avirulence protein B


Mass: 36262.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: avrB / Production host: Escherichia coli (E. coli) / References: UniProt: P13835
#2: Protein/peptide RIN4


Mass: 3428.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris (pH 7.5~7.8), 27%~32% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 82030 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 13.57 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 46.1
Reflection shellResolution: 1.29→1.34 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 7654 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→36.71 Å / SU ML: 0.1081 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.9754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1799 1991 2.45 %
Rwork0.1659 79182 -
obs0.1663 81173 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.59 Å2
Refinement stepCycle: LAST / Resolution: 1.29→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 60 334 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912648
X-RAY DIFFRACTIONf_angle_d0.98073565
X-RAY DIFFRACTIONf_chiral_restr0.0749376
X-RAY DIFFRACTIONf_plane_restr0.0107469
X-RAY DIFFRACTIONf_dihedral_angle_d6.9643372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.19581350.19245300X-RAY DIFFRACTION93.93
1.32-1.360.17881380.18715511X-RAY DIFFRACTION97.99
1.36-1.40.2221410.18625573X-RAY DIFFRACTION98.52
1.4-1.440.19931380.18345575X-RAY DIFFRACTION98.74
1.44-1.490.1671410.16795618X-RAY DIFFRACTION99
1.49-1.550.18221420.15915595X-RAY DIFFRACTION99.08
1.55-1.630.15981410.15465615X-RAY DIFFRACTION99.33
1.63-1.710.18871430.16095671X-RAY DIFFRACTION99.49
1.71-1.820.19061430.15945677X-RAY DIFFRACTION99.74
1.82-1.960.18151440.15715692X-RAY DIFFRACTION99.69
1.96-2.160.16181420.15025711X-RAY DIFFRACTION99.91
2.16-2.470.15391450.14875785X-RAY DIFFRACTION99.97
2.47-3.110.16021460.17225814X-RAY DIFFRACTION99.95
3.11-36.710.20411520.17546045X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -19.8328536441 Å / Origin y: 23.1880264633 Å / Origin z: -11.8653070889 Å
111213212223313233
T0.087449921131 Å2-0.00412525210181 Å20.00259447667518 Å2-0.0909313115427 Å2-0.00486060589274 Å2--0.0816810392753 Å2
L0.483486106971 °20.298367546538 °2-0.137573647331 °2-0.855132365801 °2-0.401814016307 °2--0.806359112701 °2
S0.0341914147652 Å °-0.0410275355036 Å °0.00168781915745 Å °0.128306450529 Å °-0.0235776864371 Å °0.043078659644 Å °-0.0649695894976 Å °0.000927479752223 Å °-0.00118664114694 Å °
Refinement TLS groupSelection details: all

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