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- PDB-6gzt: Structure of Chlamydia trachomatis effector protein ChlaDUB1 boun... -

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Basic information

Entry
Database: PDB / ID: 6gzt
TitleStructure of Chlamydia trachomatis effector protein ChlaDUB1 bound to Coenzyme A
ComponentsDeubiquitinase and deneddylase Dub1
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase / Acetyltransferase
Function / homology
Function and homology information


deNEDDylase activity / deSUMOylase activity / protein desumoylation / protein deneddylation / protein deubiquitination / host cell / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane
Similarity search - Function
Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
COENZYME A / Deubiquitinase and deneddylase Dub1
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation.
Authors: Pruneda, J.N. / Bastidas, R.J. / Bertsoulaki, E. / Swatek, K.N. / Santhanam, B. / Clague, M.J. / Valdivia, R.H. / Urbe, S. / Komander, D.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase Dub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5397
Polymers31,3071
Non-polymers1,2326
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-13 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.635, 132.635, 132.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Deubiquitinase and deneddylase Dub1 / ChlaDub1


Mass: 31307.244 Da / Num. of mol.: 1 / Fragment: UNP residues 130-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: cdu1, CTL0247 / Production host: Escherichia coli (E. coli)
References: UniProt: B0B9A0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.2), 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→66.32 Å / Num. obs: 22779 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAG

5hag


Resolution: 2.1→46.894 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2158 1086 4.77 %
Rwork0.1822 --
obs0.1838 22775 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 77 147 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042274
X-RAY DIFFRACTIONf_angle_d0.8843098
X-RAY DIFFRACTIONf_dihedral_angle_d15.066850
X-RAY DIFFRACTIONf_chiral_restr0.057338
X-RAY DIFFRACTIONf_plane_restr0.004385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.19590.32421470.26212704X-RAY DIFFRACTION100
2.1959-2.31170.28951370.23522654X-RAY DIFFRACTION100
2.3117-2.45650.27071340.21812695X-RAY DIFFRACTION100
2.4565-2.64610.22031260.20032699X-RAY DIFFRACTION100
2.6461-2.91240.23681380.19212673X-RAY DIFFRACTION100
2.9124-3.33370.20281330.18382733X-RAY DIFFRACTION100
3.3337-4.19970.17391220.15882739X-RAY DIFFRACTION100
4.1997-46.90520.19921490.16092792X-RAY DIFFRACTION100

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