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- PDB-8twj: AvrB_R266A bound with UDP -

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Basic information

Entry
Database: PDB / ID: 8twj
TitleAvrB_R266A bound with UDP
ComponentsAvirulence protein B
KeywordsTRANSFERASE / Protein complex
Function / homologyAvirulence B/C / Avirulence B/C superfamily / : / Avirulence protein / extracellular region / URIDINE-5'-DIPHOSPHATE / Avirulence protein B
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8275
Polymers36,1761
Non-polymers6504
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.830, 119.830, 63.906
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Avirulence protein B


Mass: 36176.242 Da / Num. of mol.: 1 / Mutation: R266A
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: 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
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Glycine (pH 8.9~9.5), 27%~34% 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: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41240 / % possible obs: 99.7 % / Redundancy: 12.4 % / Biso Wilson estimate: 19.73 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1180 / CC1/2: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.28 Å / SU ML: 0.1449 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1911 2007 5.97 %
Rwork0.1636 31633 -
obs0.1653 33640 81.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 41 263 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122492
X-RAY DIFFRACTIONf_angle_d1.16643381
X-RAY DIFFRACTIONf_chiral_restr0.0572364
X-RAY DIFFRACTIONf_plane_restr0.0108442
X-RAY DIFFRACTIONf_dihedral_angle_d6.935344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.2494540.2098762X-RAY DIFFRACTION27.81
1.95-20.217620.1924967X-RAY DIFFRACTION35.08
2-2.060.2212770.18241256X-RAY DIFFRACTION45.29
2.06-2.130.21141040.18281599X-RAY DIFFRACTION58.36
2.13-2.20.21251380.18142146X-RAY DIFFRACTION78.01
2.2-2.290.22211660.17322628X-RAY DIFFRACTION95.91
2.29-2.390.19011800.16022753X-RAY DIFFRACTION99.36
2.39-2.520.21131660.15742757X-RAY DIFFRACTION99.73
2.52-2.680.19641770.15352773X-RAY DIFFRACTION99.86
2.68-2.890.17331750.15762776X-RAY DIFFRACTION99.9
2.89-3.180.17551750.16642778X-RAY DIFFRACTION99.86
3.18-3.630.1781810.15722785X-RAY DIFFRACTION99.97
3.64-4.580.17231680.1422790X-RAY DIFFRACTION100
4.58-40.280.20111840.1822863X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 59.9632657636 Å / Origin y: -12.5071175337 Å / Origin z: 8.74866249181 Å
111213212223313233
T0.178735634604 Å20.0114687613054 Å2-0.036366229582 Å2-0.0355420419318 Å20.00418204363526 Å2--0.0915735712056 Å2
L0.333785924781 °2-0.0623399660847 °20.0639371031869 °2-0.162785708004 °20.0424039413287 °2--0.246702144541 °2
S0.0877630080406 Å °-0.0490673585799 Å °-0.0571150795435 Å °0.0122692004714 Å °-0.0131420898832 Å °0.0120745909755 Å °0.0698541673863 Å °-0.00552050567364 Å °0.0798861612436 Å °
Refinement TLS groupSelection details: all

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