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- PDB-3u0j: Crystal structure of ADP-ribosyltransferase HopU1 of Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3u0j
TitleCrystal structure of ADP-ribosyltransferase HopU1 of Pseudomonas syringae pv. Tomato DC3000
ComponentsType III effector HopU1
KeywordsTRANSFERASE / ADP-ribosyltransferase / GRP7
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / extracellular region
Similarity search - Function
Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Type III effector HopU1
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLin, Y. / Yang, H. / Wang, P. / Xu, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity
Authors: Jeong, B.-R. / Lin, Y. / Joe, A. / Guo, M. / Korneli, C. / Yang, H. / Wang, P. / Yu, M. / Cerny, R.L. / Staiger, D. / Alfano, J.R. / Xu, Y.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 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
B: Type III effector HopU1
A: Type III effector HopU1


Theoretical massNumber of molelcules
Total (without water)61,1542
Polymers61,1542
Non-polymers00
Water3,693205
1
B: Type III effector HopU1


Theoretical massNumber of molelcules
Total (without water)30,5771
Polymers30,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Type III effector HopU1


Theoretical massNumber of molelcules
Total (without water)30,5771
Polymers30,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.558, 92.558, 101.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Type III effector HopU1


Mass: 30577.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: hopU1, PSPTO_0501 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q88A91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M HEPES (pH 7.3), 5% PEG 10000, 8% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2010 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 23703 / Num. obs: 22825 / % possible obs: 96.25 % / Biso Wilson estimate: 26.78 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.279 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 0.07 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1170 5.13 %
Rwork0.1787 --
obs0.1804 22825 96.25 %
all-23703 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.927 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 110.08 Å2 / Biso mean: 27.4888 Å2 / Biso min: 1.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.4228 Å20 Å2-0 Å2
2--1.4228 Å20 Å2
3----4.8855 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 0 205 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013850
X-RAY DIFFRACTIONf_angle_d1.3195192
X-RAY DIFFRACTIONf_dihedral_angle_d17.5541412
X-RAY DIFFRACTIONf_chiral_restr0.08543
X-RAY DIFFRACTIONf_plane_restr0.005690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6971-2.81980.2681260.2154254190
2.8198-2.96840.26581450.1968257092
2.9684-3.15440.23911460.1886265795
3.1544-3.39780.22941470.1732269897
3.3978-3.73970.19531400.1544277499
3.7397-4.28050.19161550.1453277599
4.2805-5.39160.16011700.1363277999
5.3916-46.28580.18221410.1797286199

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