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

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Basic information

Entry
Database: PDB / ID: 5cra
TitleStructure of the SdeA DUB Domain
Components
  • Polyubiquitin-B
  • SdeA
KeywordsHYDROLASE / Deubiquitinase / Legionella
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
METHYL 4-AMINOBUTANOATE / Tail fiber / SdeA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.64 Å
AuthorsSheedlo, M.J. / Qiu, J. / 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 1.3Dec 4, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SdeA
D: Polyubiquitin-B
B: SdeA
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09215
Polymers58,9934
Non-polymers1,09911
Water57632
1
A: SdeA
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1909
Polymers29,4962
Non-polymers6947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7 kcal/mol
Surface area11520 Å2
MethodPISA
2
B: SdeA
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9026
Polymers29,4962
Non-polymers4054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-7 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.192, 64.192, 120.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASPASPAA2 - 1732 - 173
21PROPROASPASPBC2 - 1732 - 173
12METMETGLYGLYDB1 - 751 - 75
22METMETGLYGLYCD1 - 751 - 75

NCS ensembles :
ID
1
2

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Components

#1: Protein SdeA


Mass: 20976.615 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) / Strain (production host): BL21 / References: UniProt: Q6RCR0
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 2 / Fragment: UNP residues 1-75
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GVE / METHYL 4-AMINOBUTANOATE


Type: peptide-like / Mass: 117.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris:HCl, 3.0 M Sodium Chloride

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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 25, 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: 2.55→50 Å / Num. obs: 18407 / % possible obs: 90.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.1
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.6 % / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.64→40.89 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.303 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / ESU R: 3.941 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23599 843 5.2 %RANDOM
Rwork0.18437 ---
obs0.18702 15497 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.372 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.64→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 45 32 3859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193894
X-RAY DIFFRACTIONr_bond_other_d0.0020.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9765290
X-RAY DIFFRACTIONr_angle_other_deg1.05438486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7724.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50915634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0791520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02872
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4843.5141976
X-RAY DIFFRACTIONr_mcbond_other2.4843.5151973
X-RAY DIFFRACTIONr_mcangle_it3.8025.2672458
X-RAY DIFFRACTIONr_mcangle_other3.8015.2662459
X-RAY DIFFRACTIONr_scbond_it3.3483.9631918
X-RAY DIFFRACTIONr_scbond_other3.3113.951883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3295.7682773
X-RAY DIFFRACTIONr_long_range_B_refined6.93527.9564147
X-RAY DIFFRACTIONr_long_range_B_other6.93427.9534145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98520.03
12B98520.03
21D48550.01
22C48550.01
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 71 -
Rwork0.233 1123 -
obs--100 %

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