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- PDB-2oix: Xanthomonas XopD C470A Mutant -

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Basic information

Entry
Database: PDB / ID: 2oix
TitleXanthomonas XopD C470A Mutant
ComponentsXanthomonas outer protein D
KeywordsHYDROLASE / Clan CE Family 48 Cysteine protease / Type III secreted effector / deSUMOylating enzyme / secreted virulence facter / peptidase activity / isopeptidase activity
Function / homology
Function and homology information


deNEDDylase activity / cysteine-type peptidase activity / proteolysis
Similarity search - Function
NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Xanthomonas outer protein D
Similarity search - Component
Biological speciesXanthomonas euvesicatoria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsChosed, R. / Tomchick, D.R. / Brautigam, C.A. / Machius, M. / Orth, K.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural analysis of Xanthomonas XopD provides insights into substrate specificity of ubiquitin-like protein proteases.
Authors: Chosed, R. / Tomchick, D.R. / Brautigam, C.A. / Mukherjee, S. / Negi, V.S. / Machius, M. / Orth, K.
#1: Journal: Biochem.J. / Year: 2006
Title: Evolution of a signalling system that incorporates both redundancy and diversity: Arabidopsis SUMOylation.
Authors: Chosed, R. / Mukherjee, S. / Lois, L.M. / Orth, K.
#2: Journal: Mol.Microbiol. / Year: 2003
Title: Xanthomonas type III effector XopD targets SUMO-conjugated proteins in planta.
Authors: Hotson, A. / Chosed, R. / Shu, H. / Orth, K. / Mudgett, M.B.
#3: Journal: Mol.Cell / Year: 2000
Title: Ulp1-SUMO Crystal Structure and Genetic Analysis Reveal Conserved Interactions and a Regulatory Element Essential for Cell Growth in Yeast
Authors: Mossessova, E. / Lima, C.D.
History
DepositionJan 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthomonas outer protein D


Theoretical massNumber of molelcules
Total (without water)20,7311
Polymers20,7311
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.953, 91.953, 45.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Xanthomonas outer protein D


Mass: 20731.051 Da / Num. of mol.: 1
Fragment: catalytic fragment, inactive mutant (Residues 335-520)
Mutation: C470A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas euvesicatoria (bacteria) / Gene: xopD / Plasmid: pGEX-rTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: Q3BYJ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15 mg/mL protein in 20 mM Tris-HCl pH 7.5, 75 mM KCl, and 0.5 mM DTT and 1.4 - 1.6 M sodium potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97905 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 24, 2005 / Details: None
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.8→25.33 Å / Num. all: 17346 / Num. obs: 17346 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 30.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.95 / % possible all: 77.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2OIV

2oiv


Resolution: 1.8→25.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.85 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25903 513 3 %RANDOM
Rwork0.21047 ---
all0.21191 17317 --
obs0.21191 16804 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.158 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.148 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 91 1499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9481958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33923.50677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8761514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021133
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2954
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0841.5904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70321417
X-RAY DIFFRACTIONr_scbond_it2.3773597
X-RAY DIFFRACTIONr_scangle_it3.4684.5541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 28 -
Rwork0.281 987 -
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)
18.07424.8365-10.820719.4344-7.790214.6049-0.08491.34980.2634-1.35320.80491.61470.1696-2.1068-0.720.0977-0.1566-0.13440.25390.00720.0019-34.022440.71593.2395
22.79380.581-0.21051.60250.13663.3337-0.11530.2666-0.431-0.06110.0315-0.39780.51040.01760.08380.1477-0.0190.01430.0244-0.02250.1145-19.370836.904212.1477
327.40273.0554-1.93830.50950.80558.97220.5673-1.1769-0.81430.8351-0.58370.01311.5172-0.79530.01640.3913-0.242-0.01560.04320.027-0.1315-30.512736.33927.035
44.2944-0.13350.73733.2276-0.86882.44130.0065-0.2572-0.030.0784-0.02640.07920.1465-0.12280.020.1224-0.0126-0.00720.1291-0.01070.046-22.91646.913918.5106
532.516810.7212-8.87597.90433.879813.02541.26840.55752.56630.0449-0.99182.7311-1.1438-0.8753-0.27660.17760.0999-0.0170.20210.04970.1758-33.668158.43979.3445
64.2811-0.5098-0.16522.56-0.18383.96150.0807-0.20660.38430.0702-0.05790.1522-0.0949-0.004-0.02280.0743-0.0070.01140.0573-0.06370.0943-28.326153.130621.2439
75.37062.65720.03332.72660.77123.3587-0.2040.31530.0855-0.26220.0621-0.0626-0.0453-0.07080.14190.1421-0.03140.00470.11060.03530.0363-17.367249.73858.4038
89.37345.28910.97499.3872.8598.368-0.68661.2864-0.4237-1.40750.67410.08310.3079-0.02350.01250.1424-0.15930.02330.23760.0201-0.1094-22.616242.5339-1.8924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA336 - 3432 - 9
2X-RAY DIFFRACTION2AA344 - 37410 - 40
3X-RAY DIFFRACTION3AA375 - 39341 - 59
4X-RAY DIFFRACTION4AA394 - 42960 - 95
5X-RAY DIFFRACTION5AA430 - 43596 - 101
6X-RAY DIFFRACTION6AA436 - 463102 - 129
7X-RAY DIFFRACTION7AA464 - 499130 - 165
8X-RAY DIFFRACTION8AA500 - 515166 - 181

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