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- PDB-8two: AvrB bound with UDP and RIN4_T166-Rha -

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Basic information

Entry
Database: PDB / ID: 8two
TitleAvrB bound with UDP and RIN4_T166-Rha
Components
  • Avirulence protein B
  • RPM1-interacting protein 4
KeywordsTRANSFERASE / Protein complex
Function / homologyAvirulence B/C / Avirulence B/C superfamily / Avirulence protein / extracellular region / alpha-L-rhamnopyranose / URIDINE-5'-DIPHOSPHATE / Avirulence protein B
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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)40,2594
Polymers39,6912
Non-polymers5682
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-23 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 119.236, 39.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
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

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: 2.09→52.15 Å / Num. obs: 16986 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 49.65 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.61
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 828 / CC1/2: 0.233

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→52.15 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 1661 10 %
Rwork0.2205 --
obs0.2275 16606 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 35 0 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172608
X-RAY DIFFRACTIONf_angle_d1.5543547
X-RAY DIFFRACTIONf_dihedral_angle_d7.905353
X-RAY DIFFRACTIONf_chiral_restr0.07383
X-RAY DIFFRACTIONf_plane_restr0.015465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.43361210.42491093X-RAY DIFFRACTION89
2.16-2.230.41871300.36761169X-RAY DIFFRACTION93
2.23-2.30.35631290.3631152X-RAY DIFFRACTION93
2.3-2.40.38191360.31751225X-RAY DIFFRACTION98
2.4-2.510.36241410.29491279X-RAY DIFFRACTION100
2.51-2.640.2991380.27241239X-RAY DIFFRACTION100
2.64-2.80.35191390.26131259X-RAY DIFFRACTION100
2.8-3.020.31921410.23221271X-RAY DIFFRACTION100
3.02-3.320.28351440.21821284X-RAY DIFFRACTION100
3.32-3.80.2741410.19341274X-RAY DIFFRACTION100
3.8-4.790.2411450.18611305X-RAY DIFFRACTION100
4.79-52.150.27681560.18671395X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.4834 Å / Origin y: 22.8961 Å / Origin z: 9.8324 Å
111213212223313233
T0.3324 Å20.0036 Å2-0.0224 Å2-0.3257 Å20.0195 Å2--0.2805 Å2
L1.8347 °20.3574 °2-0.4156 °2-0.944 °2-0.4167 °2--0.2916 °2
S-0.035 Å °0.105 Å °-0.0555 Å °0.0229 Å °0.0298 Å °0.1937 Å °-0.0235 Å °0.0533 Å °-0 Å °
Refinement TLS groupSelection details: all

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