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- PDB-8tws: AvrB bound with UDP-rhamnose and RIN4 C-NOI motif -

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Basic information

Entry
Database: PDB / ID: 8tws
TitleAvrB bound with UDP-rhamnose and RIN4 C-NOI motif
Components
  • Avirulence protein B
  • RPM1-interacting protein 4
KeywordsTRANSFERASE / Protein complex
Function / homologyAvirulence B/C / Avirulence B/C superfamily / : / Avirulence protein / extracellular region / Chem-AWU / Avirulence protein B
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 21, 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: RPM1-interacting protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2413
Polymers39,6912
Non-polymers5501
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-16 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.622, 123.580, 45.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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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 RPM1-interacting protein 4


Mass: 3428.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RIN4, At3g25070, MJL12_1 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-AWU / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 550.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.82 %
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: ALS / Beamline: 2.0.1 / Wavelength: 1.0358 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0358 Å / Relative weight: 1
ReflectionResolution: 2.85→52.97 Å / Num. obs: 8193 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 60.96 Å2 / CC1/2: 0.925 / Net I/σ(I): 2
Reflection shellResolution: 2.85→2.9 Å / Num. unique obs: 375 / CC1/2: 0.038

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→52.97 Å / SU ML: 0.5189 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3355 777 10.02 %
Rwork0.2797 6980 -
obs0.2853 7757 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.69 Å2
Refinement stepCycle: LAST / Resolution: 2.85→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 35 0 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362609
X-RAY DIFFRACTIONf_angle_d0.76373550
X-RAY DIFFRACTIONf_chiral_restr0.0406384
X-RAY DIFFRACTIONf_plane_restr0.0076465
X-RAY DIFFRACTIONf_dihedral_angle_d15.7073366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.37221040.3821932X-RAY DIFFRACTION78.72
3.03-3.260.4241210.37591091X-RAY DIFFRACTION90.25
3.26-3.590.38761320.33251195X-RAY DIFFRACTION99.85
3.59-4.110.36921360.28381222X-RAY DIFFRACTION100
4.11-5.180.28561370.2421228X-RAY DIFFRACTION99.78
5.18-52.970.29621470.23511312X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 20.354031145 Å / Origin y: 24.1471272901 Å / Origin z: 11.7471800512 Å
111213212223313233
T0.239970013174 Å20.025976927617 Å2-0.0189076078435 Å2-0.242921140481 Å20.00710898859991 Å2--0.205294404771 Å2
L0.0616765367754 °2-0.00609693463664 °2-0.0254104034345 °2-0.0141584140127 °2-0.0249143408282 °2--0.0378877762124 °2
S0.0923743243135 Å °0.00842471507165 Å °-0.120102962879 Å °-0.0549270560579 Å °-0.0584452918947 Å °0.010275879382 Å °0.0166868389839 Å °-0.0945152309142 Å °0.00019540059025 Å °
Refinement TLS groupSelection details: all

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