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- PDB-5jp1: Structure of Xanthomonas campestris effector protein XopD bound t... -

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Basic information

Entry
Database: PDB / ID: 5jp1
TitleStructure of Xanthomonas campestris effector protein XopD bound to tomato SUMO
Components
  • Small ubiquitin-related modifier
  • Xanthomonas outer protein D
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase / DeSUMOylase
Function / homology
Function and homology information


deNEDDylase activity / ubiquitin-like protein ligase binding / protein sumoylation / cysteine-type peptidase activity / protein tag activity / proteolysis / nucleus
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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues ...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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / MALONATE ION / Xanthomonas outer protein D / Small ubiquitin-related modifier
Similarity search - Component
Biological speciesXanthomonas campestris pv. vesicatoria (bacteria)
Solanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases.
Authors: Pruneda, J.N. / Durkin, C.H. / Geurink, P.P. / Ovaa, H. / Santhanam, B. / Holden, D.W. / Komander, D.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthomonas outer protein D
B: Small ubiquitin-related modifier
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6745
Polymers35,3172
Non-polymers3563
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint3 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.103, 119.103, 50.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-848-

HOH

21B-212-

HOH

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Components

#1: Protein Xanthomonas outer protein D


Mass: 24438.215 Da / Num. of mol.: 1 / Fragment: UNP residues 298-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. vesicatoria (strain 85-10) (bacteria)
Gene: xopD, XCV0437 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3BYJ5
#2: Protein Small ubiquitin-related modifier / SUMO


Mass: 10879.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: sumo / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SMD1
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M bicine (pH 9.0) 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.1→59.55 Å / Num. obs: 23605 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIV, 1TGZ

2oiv

1tgz


Resolution: 2.1→59.551 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1281 5.43 %
Rwork0.1813 --
obs0.1832 23602 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→59.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 22 199 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022245
X-RAY DIFFRACTIONf_angle_d0.5073051
X-RAY DIFFRACTIONf_dihedral_angle_d17.5591365
X-RAY DIFFRACTIONf_chiral_restr0.043333
X-RAY DIFFRACTIONf_plane_restr0.004414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.27251220.24782486X-RAY DIFFRACTION99
2.1841-2.28350.2661350.222362X-RAY DIFFRACTION94
2.2835-2.40390.2551320.2112499X-RAY DIFFRACTION99
2.4039-2.55450.25521430.20892482X-RAY DIFFRACTION99
2.5545-2.75180.231590.21172514X-RAY DIFFRACTION99
2.7518-3.02870.25071610.20772444X-RAY DIFFRACTION99
3.0287-3.46690.23281460.17322440X-RAY DIFFRACTION96
3.4669-4.36770.1711580.13362520X-RAY DIFFRACTION100
4.3677-59.57540.17171250.16282574X-RAY DIFFRACTION97
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)
11.5305-0.30840.05461.5009-0.39281.8111-0.00710.12910.177-0.0505-0.00630.069-0.0574-0.05170.01480.13970.013-0.00710.11640.00840.139949.181513.8391-2.147
24.82572.336-1.84123.7374-1.33323.3329-0.0798-0.1746-0.09710.30640.02460.29770.1557-0.2440.06780.2190.01790.03750.1711-0.00230.187742.1295-3.364513.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 319 through 514)
2X-RAY DIFFRACTION2(chain 'B' and resid 19 through 96)

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