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- PDB-2fd4: Crystal Structure of AvrPtoB (436-553) -

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Basic information

Entry
Database: PDB / ID: 2fd4
TitleCrystal Structure of AvrPtoB (436-553)
Componentsavirulence protein AvrptoB
KeywordsLIGASE / Pseudomonas / AvrPtoB / RING finger / U-box / ubiquitin ligase
Function / homology
Function and homology information


effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host programmed cell death / Transferases; Acyltransferases; Aminoacyltransferases / transferase activity / extracellular region
Similarity search - Function
AvrPtoB, C-terminal domain / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Effector protein HopAB2
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJanjusevic, R. / Stebbins, C.E.
CitationJournal: Science / Year: 2006
Title: A bacterial inhibitor of host programmed cell death defenses is an E3 ubiquitin ligase.
Authors: Janjusevic, R. / Abramovitch, R.B. / Martin, G.B. / Stebbins, C.E.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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
A: avirulence protein AvrptoB


Theoretical massNumber of molelcules
Total (without water)13,2871
Polymers13,2871
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.863, 61.863, 60.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein avirulence protein AvrptoB


Mass: 13286.791 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 436-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RSY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.37 M-1.39 M sodium citrate, 100 mM HEPES, 2 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2004
RadiationMonochromator: Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 11.7 % / Number: 13351 / Rmerge(I) obs: 0.064 / Χ2: 1.077 / D res high: 2.2 Å / D res low: 99 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.749999.310.031.45211.6
3.764.7410010.0321.06911.8
3.293.7610010.0471.05411.8
2.993.2910010.091.01611.8
2.772.9910010.1210.97411.8
2.612.7710010.2010.96911.7
2.482.6110010.2880.97911.7
2.372.4810010.3921.03411.7
2.282.3710010.4751.02211.7
2.22.2810010.6271.20411.6
ReflectionResolution: 1.7→50 Å / Num. obs: 15065 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.03
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.765.10.674199.9
1.76-1.835.10.4751100
1.83-1.915.10.272199.9
1.91-2.025.10.1491100
2.02-2.145.10.0921100
2.14-2.315.10.061199.9
2.31-2.5460.053199.8
2.54-2.919.20.0551100
2.91-3.665.40.031100
3.66-995.10.022199.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.2 Å / D res low: 99 Å / FOM : 0.32 / Reflection: 7159
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se54.2910.2220.6810.0041.99
2Se600.5870.1490.0921.343
3Se600.2830.7240.1071.37
Phasing MAD shell
Resolution (Å)FOM Reflection
8.02-990.4342
5.03-8.020.48610
3.92-5.030.49762
3.32-3.920.46886
2.93-3.320.391015
2.65-2.930.291097
2.44-2.650.191176
2.27-2.440.131271
Phasing dmFOM : 0.58 / FOM acentric: 0.59 / FOM centric: 0.57 / Reflection: 7161 / Reflection acentric: 6141 / Reflection centric: 1020
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-26.9520.910.940.85333221112
3.9-6.30.90.930.77988790198
3.1-3.90.840.860.7212111025186
2.8-3.10.650.670.5512051052153
2.4-2.80.410.420.3521291888241
2.2-2.40.250.250.2512951165130

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.825 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26669 637 5 %RANDOM
Rwork0.24215 ---
obs0.24344 12049 99.42 %-
all-12686 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.173 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 51 852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022814
X-RAY DIFFRACTIONr_bond_other_d0.0030.02742
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9821097
X-RAY DIFFRACTIONr_angle_other_deg0.89431737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9125101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21325.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33815139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.097153
X-RAY DIFFRACTIONr_chiral_restr0.1220.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_nbd_refined0.2390.2159
X-RAY DIFFRACTIONr_nbd_other0.1960.2736
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2380
X-RAY DIFFRACTIONr_nbtor_other0.0940.2507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1471.5656
X-RAY DIFFRACTIONr_mcbond_other0.2931.5211
X-RAY DIFFRACTIONr_mcangle_it1.372832
X-RAY DIFFRACTIONr_scbond_it2.453327
X-RAY DIFFRACTIONr_scangle_it3.5254.5265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 42 -
Rwork0.314 880 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.611-0.6124-0.73677.65051.327815.4869-0.1684-0.16420.0710.14970.6088-0.58490.1423-0.2376-0.4404-0.2210.0113-0.0043-0.20440.0087-0.124231.45063.89888.2231
239.1359-3.387124.486711.69884.54445.54360.29881.57990.845-1.2903-0.099-1.14190.98093.6556-0.19980.10680.04150.32860.09030.04010.36646.23783.5153-3.878
34.92910.37472.83097.221-2.48179.193-0.06470.2081-0.5116-0.29280.2531-0.80060.39950.3931-0.1885-0.1486-0.01120.0755-0.1915-0.0732-0.034438.05926.2247-0.8922
43.5991-0.9998-0.05697.6642-1.73237.6723-0.35950.0763-0.0775-0.25160.51-0.2532-0.199-0.5738-0.1505-0.177-0.0522-0.0007-0.174-0.0252-0.197430.871610.93290.1969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA435 - 4544 - 23
2X-RAY DIFFRACTION2AA461 - 46730 - 36
3X-RAY DIFFRACTION3AA472 - 50741 - 76
4X-RAY DIFFRACTION4AA513 - 55382 - 122

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