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- PDB-5crc: Structure of the SdeA DUB Domain -

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Basic information

Entry
Database: PDB / ID: 5crc
TitleStructure of the SdeA DUB Domain
ComponentsSdeA
KeywordsHYDROLASE / Deubiquitinase / Legionella
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / nucleotide binding
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain
Similarity search - Domain/homology
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.853 Å
AuthorsSheedlo, M.J. / Qiu, J. / Tan, Y. / Paul, L.N. / Luo, Z.Q. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.
Authors: Sheedlo, M.J. / Qiu, J. / Tan, Y. / Paul, L.N. / Luo, Z.Q. / Das, C.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.country / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: SdeA
B: SdeA


Theoretical massNumber of molelcules
Total (without water)42,7042
Polymers42,7042
Non-polymers00
Water00
1
A: SdeA


Theoretical massNumber of molelcules
Total (without water)21,3521
Polymers21,3521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SdeA


Theoretical massNumber of molelcules
Total (without water)21,3521
Polymers21,3521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-61 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.542, 63.340, 136.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SdeA


Mass: 21351.777 Da / Num. of mol.: 2 / Fragment: DUB domain (residues 6-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR0
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: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris:HCl, 3.0 M Sodium Chloride, 3% Methyl-2,4-Pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2015
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→36.96 Å / Num. obs: 7153 / % possible obs: 90.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.264 / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.853→36.955 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2957 647 9.05 %
Rwork0.2802 --
obs0.2804 7153 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.853→36.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 0 0 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062322
X-RAY DIFFRACTIONf_angle_d1.4743162
X-RAY DIFFRACTIONf_dihedral_angle_d15.957822
X-RAY DIFFRACTIONf_chiral_restr0.082346
X-RAY DIFFRACTIONf_plane_restr0.005419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.855-3.59590.31571590.30133217X-RAY DIFFRACTION84
3.5959-28.71630.28271600.26493603X-RAY DIFFRACTION90

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