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- PDB-2oiv: Structural Analysis of Xanthomonas XopD Provides Insights Into Su... -

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Basic information

Entry
Database: PDB / ID: 2oiv
TitleStructural Analysis of Xanthomonas XopD Provides Insights Into Substrate Specificity of Ubiquitin-like Protein Proteases
ComponentsXanthomonas outer protein D
KeywordsHYDROLASE / Clan CE Family 48 Cysteine protease / Type III secreted effector / deSUMOylating enzyme / secreted virulence factor / peptidase / isopeptidase
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / cysteine-type peptidase activity / proteolysis
Similarity search - Function
NEDD8-specific protease 1/2-like / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Xanthomonas outer protein D
Similarity search - Component
Biological speciesXanthomonas euvesicatoria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthomonas outer protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8582
Polymers20,7631
Non-polymers951
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.618, 91.618, 44.820
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: 20763.115 Da / Num. of mol.: 1 / Fragment: catalytic fragment (Residues 335-520)
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
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, 1.4 - 1.6 M sodium potassium phosphate, 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: 0.97929 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 17, 2004
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.95→32.04 Å / Num. all: 14282 / Num. obs: 14282 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→32.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.92 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25017 720 5 %RANDOM
Rwork0.20795 ---
all0.21012 14274 --
obs0.21012 13554 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: 42.341 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---1.33 Å20 Å2
3---2.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.165 Å0.185 Å
Refinement stepCycle: LAST / Resolution: 1.95→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 5 83 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211384
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9571882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80323.37874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5151514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021085
X-RAY DIFFRACTIONr_nbd_refined0.2020.2619
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.25
X-RAY DIFFRACTIONr_mcbond_it1.0331.5872
X-RAY DIFFRACTIONr_mcangle_it1.64221354
X-RAY DIFFRACTIONr_scbond_it2.3673576
X-RAY DIFFRACTIONr_scangle_it3.454.5528
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 49 -
Rwork0.286 982 -
obs-982 100 %
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)
11.4638-0.84240.38032.55620.18453.02590.03340.24920.1564-0.2811-0.1575-0.2446-0.01480.39490.1240.06190.01350.01310.18170.01870.13598.631624.6075-0.5502
23.6276-1.28280.44483.6203-0.02162.0725-0.1593-0.1937-0.15150.2760.12550.03960.19720.27510.03380.130.01620.0330.14160.00720.09512.413920.40489.892
36.66324.3445-1.75216.07353.398412.3611-0.05530.4337-0.325-0.4993-0.33920.1666-0.0648-0.93920.39440.09710.02890.05270.0774-0.00030.1535-8.477612.03495.3944
44.4466-0.74191.56425.1153-0.61724.5749-0.0988-0.0473-0.25040.3020.12350.6011-0.0989-0.1508-0.02480.069-0.00960.07030.0891-0.00350.1326-7.444320.079410.4912
55.0515-3.0811-0.21383.8361-0.21262.50790.04710.2304-0.0344-0.2388-0.18170.1710.01930.04440.13470.09490.0026-0.03230.13490.03170.1158-3.412930.4521-1.8809
650.3645-8.8132-8.34595.17230.968810.83720.62693.598-0.1901-1.4521-0.7136-0.36140.1452-0.38250.08670.37920.10930.00960.14980.083-0.23492.700123.8062-13.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA338 - 3734 - 39
2X-RAY DIFFRACTION2AA374 - 42940 - 95
3X-RAY DIFFRACTION3AA430 - 44396 - 109
4X-RAY DIFFRACTION4AA444 - 463110 - 129
5X-RAY DIFFRACTION5AA469 - 499135 - 165
6X-RAY DIFFRACTION6AA500 - 514166 - 180

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