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- PDB-5yim: Structure of a Legionella effector -

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Basic information

Entry
Database: PDB / ID: 5yim
TitleStructure of a Legionella effector
ComponentsSdeA
KeywordsTRANSFERASE / monomer / multi-domain protein
Function / homologySidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / NAD+-protein-arginine ADP-ribosyltransferase activity / SdeA
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.394 Å
AuthorsFeng, Y. / Dong, Y. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670766 China
CitationJournal: Nature / Year: 2018
Title: Structural basis of ubiquitin modification by the Legionella effector SdeA.
Authors: Dong, Y. / Mu, Y. / Xie, Y. / Zhang, Y. / Han, Y. / Zhou, Y. / Wang, W. / Liu, Z. / Wu, M. / Wang, H. / Pan, M. / Xu, N. / Xu, C.Q. / Yang, M. / Fan, S. / Deng, H. / Tan, T. / Liu, X. / Liu, ...Authors: Dong, Y. / Mu, Y. / Xie, Y. / Zhang, Y. / Han, Y. / Zhou, Y. / Wang, W. / Liu, Z. / Wu, M. / Wang, H. / Pan, M. / Xu, N. / Xu, C.Q. / Yang, M. / Fan, S. / Deng, H. / Tan, T. / Liu, X. / Liu, L. / Li, J. / Wang, J. / Fang, X. / Feng, Y.
History
DepositionOct 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SdeA
C: SdeA


Theoretical massNumber of molelcules
Total (without water)217,5542
Polymers217,5542
Non-polymers00
Water0
1
A: SdeA


Theoretical massNumber of molelcules
Total (without water)108,7771
Polymers108,7771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SdeA


Theoretical massNumber of molelcules
Total (without water)108,7771
Polymers108,7771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.650, 295.430, 194.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SdeA


Mass: 108776.883 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 236-1194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR0

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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: 4.61 Å3/Da / Density % sol: 73.34 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 55636 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 14.8
Reflection shellResolution: 3.39→3.52 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.394→50 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 30.05 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2871 5407 5.07 %
Rwork0.2507 --
obs0.2526 55636 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.394→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14129 0 0 0 14129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414356
X-RAY DIFFRACTIONf_angle_d0.95119395
X-RAY DIFFRACTIONf_dihedral_angle_d14.0635315
X-RAY DIFFRACTIONf_chiral_restr0.0362191
X-RAY DIFFRACTIONf_plane_restr0.0042554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3945-3.4330.45251740.39442789X-RAY DIFFRACTION83
3.433-3.47340.43111990.37733441X-RAY DIFFRACTION100
3.4734-3.51580.37471610.34083359X-RAY DIFFRACTION100
3.5158-3.56030.37831860.33323401X-RAY DIFFRACTION100
3.5603-3.60720.32611830.30883439X-RAY DIFFRACTION100
3.6072-3.65660.33831640.30273381X-RAY DIFFRACTION100
3.6566-3.70880.33211790.2883410X-RAY DIFFRACTION100
3.7088-3.76420.32741930.27073373X-RAY DIFFRACTION100
3.7642-3.8230.27441680.273414X-RAY DIFFRACTION100
3.823-3.88570.28721420.26833485X-RAY DIFFRACTION100
3.8857-3.95270.31381610.27483369X-RAY DIFFRACTION100
3.9527-4.02460.30881980.27223424X-RAY DIFFRACTION100
4.0246-4.1020.28521710.25933410X-RAY DIFFRACTION100
4.102-4.18570.30651850.25063397X-RAY DIFFRACTION100
4.1857-4.27670.28292100.25233367X-RAY DIFFRACTION100
4.2767-4.37620.30921900.2343378X-RAY DIFFRACTION100
4.3762-4.48560.24462020.22923397X-RAY DIFFRACTION100
4.4856-4.60690.27351500.22573424X-RAY DIFFRACTION100
4.6069-4.74250.23621750.23083404X-RAY DIFFRACTION100
4.7425-4.89560.33881780.23743418X-RAY DIFFRACTION100
4.8956-5.07050.3032280.24343340X-RAY DIFFRACTION100
5.0705-5.27350.28711540.2523464X-RAY DIFFRACTION100
5.2735-5.51350.32452110.25833325X-RAY DIFFRACTION100
5.5135-5.80420.31271950.27693401X-RAY DIFFRACTION100
5.8042-6.16780.35341770.27663390X-RAY DIFFRACTION100
6.1678-6.6440.29761330.27553429X-RAY DIFFRACTION99
6.644-7.31240.27711860.24163394X-RAY DIFFRACTION99
7.3124-8.37020.22231660.2173342X-RAY DIFFRACTION99
8.3702-10.54410.20681860.1823369X-RAY DIFFRACTION99
10.5441-105.96930.27622020.26283220X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 5.2761 Å / Origin y: 36.4883 Å / Origin z: 198.5869 Å
111213212223313233
T0.863 Å2-0.0715 Å20.0818 Å2-0.7283 Å2-0.0292 Å2--0.8882 Å2
L0.2699 °2-0.0385 °2-0.0524 °2-0.1308 °20.0348 °2--0.4688 °2
S-0.0667 Å °0.133 Å °-0.0196 Å °-0.0555 Å °0.0443 Å °-0.1496 Å °-0.0736 Å °0.0989 Å °0.013 Å °
Refinement TLS groupSelection details: all

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