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- PDB-5jp3: Structure of Xanthomonas campestris effector protein XopD bound t... -

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Basic information

Entry
Database: PDB / ID: 5jp3
TitleStructure of Xanthomonas campestris effector protein XopD bound to ubiquitin
Components
  • Polyubiquitin-B
  • Xanthomonas outer protein D
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase / DeSUMOylase
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor ...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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Ubiquitin family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Xanthomonas outer protein D
Similarity search - Component
Biological speciesXanthomonas campestris pv. vesicatoria (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthomonas outer protein D
C: Xanthomonas outer protein D
E: Xanthomonas outer protein D
B: Polyubiquitin-B
D: Polyubiquitin-B
H: Polyubiquitin-B
G: Xanthomonas outer protein D
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)131,9888
Polymers131,9888
Non-polymers00
Water79344
1
A: Xanthomonas outer protein D
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)32,9972
Polymers32,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-8 kcal/mol
Surface area13800 Å2
MethodPISA
2
C: Xanthomonas outer protein D
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)32,9972
Polymers32,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area12910 Å2
MethodPISA
3
E: Xanthomonas outer protein D
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)32,9972
Polymers32,9972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-5 kcal/mol
Surface area13060 Å2
MethodPISA
4
H: Polyubiquitin-B
G: Xanthomonas outer protein D


Theoretical massNumber of molelcules
Total (without water)32,9972
Polymers32,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.748, 132.281, 117.310
Angle α, β, γ (deg.)90.00, 105.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Xanthomonas outer protein D


Mass: 24438.215 Da / Num. of mol.: 4 / Fragment: UNP residues 298-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. vesicatoria (strain 85-10) (bacteria)
Strain: 85-10 / Gene: xopD, XCV0437 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3BYJ5
#2: Protein
Polyubiquitin-B


Mass: 8558.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M CHES (pH 9.5) 1.0M sodium citrate

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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: 2.9→43.3 Å / Num. obs: 37920 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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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, 1UBQ

2oiv

1ubq


Resolution: 2.9→43.297 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.2851 1835 4.84 %
Rwork0.241 --
obs0.2431 37909 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8192 0 0 44 8236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058365
X-RAY DIFFRACTIONf_angle_d0.82811434
X-RAY DIFFRACTIONf_dihedral_angle_d16.125043
X-RAY DIFFRACTIONf_chiral_restr0.051316
X-RAY DIFFRACTIONf_plane_restr0.0071528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97840.34691400.28462755X-RAY DIFFRACTION99
2.9784-3.0660.29331450.26762760X-RAY DIFFRACTION99
3.066-3.1650.31671460.25672779X-RAY DIFFRACTION99
3.165-3.2780.34461530.25212771X-RAY DIFFRACTION99
3.278-3.40920.29041550.25382757X-RAY DIFFRACTION99
3.4092-3.56430.29981360.24972678X-RAY DIFFRACTION96
3.5643-3.75210.32961370.26642770X-RAY DIFFRACTION99
3.7521-3.98710.31371320.23222805X-RAY DIFFRACTION100
3.9871-4.29470.24951550.21812793X-RAY DIFFRACTION100
4.2947-4.72640.26081390.20472805X-RAY DIFFRACTION99
4.7264-5.40920.26161230.22382742X-RAY DIFFRACTION97
5.4092-6.81070.27381430.26342822X-RAY DIFFRACTION100
6.8107-43.30170.24241310.23552837X-RAY DIFFRACTION98
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)
12.03810.8701-0.45251.2648-0.50411.9529-0.1096-0.056-0.31840.00160.0127-0.11830.0502-0.06140.04940.0636-0.01980.02250.070.02210.1086136.9676-21.6945135.6819
21.97960.88040.0361.86090.11491.3157-0.07420.0436-0.153-0.10430.0890.02660.1370.05940.00150.1648-0.1947-0.00170.06720.03250.1558105.5446-45.9621143.9843
32.2867-0.34710.11943.15770.02712.35940.14440.40870.8471-0.1245-0.04840.6638-0.3532-0.3263-0.01670.1640.04770.01880.37080.12760.575110.16336.3962138.2684
41.61020.5565-0.52682.8466-0.54892.66890.09260.09470.0793-0.1906-0.1362-0.2292-0.27830.5320.07220.0862-0.072-0.00920.2547-0.04360.1605153.3472-4.3757122.1277
52.66020.2974-0.76741.38950.08183.32420.0637-0.399-0.12190.5970.66911.14440.0611-0.5384-0.47020.4601-0.08070.1340.44770.1930.457587.5793-61.5369159.9082
65.65250.8161-1.95361.626-1.51651.6825-0.0672-0.827-0.8979-0.09390.43940.49110.6977-1.0149-0.06840.3861-0.2031-0.06490.98350.21840.475677.9187-34.5509179.8914
72.15660.3254-0.80251.86090.05612.64940.04730.10480.1516-0.21910.35550.0794-0.4719-0.3653-0.23550.04040.02080.06870.3771-0.04810.190594.7457-16.5971166.6012
80.83510.1354-1.05493.2658-0.61861.39190.29550.99371.7792-0.77210.1530.0075-0.59660.0081-0.26160.7416-0.03760.11550.73390.41051.0643130.699321.5462125.0333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 311 through 515)
2X-RAY DIFFRACTION2(chain 'C' and resid 320 through 515)
3X-RAY DIFFRACTION3(chain 'E' and resid 323 through 515)
4X-RAY DIFFRACTION4(chain 'B' and resid 1 through 76)
5X-RAY DIFFRACTION5(chain 'D' and resid 1 through 76)
6X-RAY DIFFRACTION6(chain 'H' and resid 1 through 76)
7X-RAY DIFFRACTION7(chain 'G' and resid 320 through 515)
8X-RAY DIFFRACTION8(chain 'F' and resid 1 through 76)

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