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- PDB-5h60: Structure of Transferase mutant-C23S,C199S -

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Basic information

Entry
Database: PDB / ID: 5h60
TitleStructure of Transferase mutant-C23S,C199S
ComponentsTransferase
KeywordsTRANSFERASE
Function / homologyprotein-arginine N-acetylglucosaminyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / toxin activity / extracellular region / metal ion binding / : / URIDINE-5'-DIPHOSPHATE / Protein-arginine N-acetylglucosaminyltransferase SseK1
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.64 Å
AuthorsPark, J.B. / Yoo, Y. / Kim, J.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for arginine glycosylation of host substrates by bacterial effector proteins.
Authors: Park, J.B. / Kim, Y.H. / Yoo, Y. / Kim, J. / Jun, S.H. / Cho, J.W. / El Qaidi, S. / Walpole, S. / Monaco, S. / Garcia-Garcia, A.A. / Wu, M. / Hays, M.P. / Hurtado-Guerrero, R. / Angulo, J. / ...Authors: Park, J.B. / Kim, Y.H. / Yoo, Y. / Kim, J. / Jun, S.H. / Cho, J.W. / El Qaidi, S. / Walpole, S. / Monaco, S. / Garcia-Garcia, A.A. / Wu, M. / Hays, M.P. / Hurtado-Guerrero, R. / Angulo, J. / Hardwidge, P.R. / Shin, J.S. / Cho, H.S.
History
DepositionNov 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.3Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3413
Polymers38,8821
Non-polymers4592
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.940, 115.940, 100.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Transferase


Mass: 38882.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L9J3*PLUS
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 290 K / Method: evaporation, recrystallization / pH: 7
Details: 0.1M Bis-Tris propane-HCl (pH 7.0), 1.0M ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→70 Å / Num. obs: 4558 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 28.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 3.64→44.87 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.886 / SU B: 45.995 / SU ML: 0.649 / Cross valid method: THROUGHOUT / ESU R Free: 0.781 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28485 244 5.1 %RANDOM
Rwork0.25352 ---
obs0.25513 4558 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 96.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 3.64→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 26 0 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192554
X-RAY DIFFRACTIONr_bond_other_d0.0070.022359
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9663447
X-RAY DIFFRACTIONr_angle_other_deg1.1135449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5765303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47625.075134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.18515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8981511
X-RAY DIFFRACTIONr_chiral_restr0.080.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022896
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02601
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_it69.4941215
X-RAY DIFFRACTIONr_mcbond_other6.0019.4851214
X-RAY DIFFRACTIONr_mcangle_it9.91314.2221517
X-RAY DIFFRACTIONr_mcangle_other9.9114.2341518
X-RAY DIFFRACTIONr_scbond_it5.069.9131337
X-RAY DIFFRACTIONr_scbond_other5.069.9131336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.64814.7111930
X-RAY DIFFRACTIONr_long_range_B_refined15.65510511
X-RAY DIFFRACTIONr_long_range_B_other15.65410512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.64→3.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 14 -
Rwork0.315 344 -
obs--99.72 %

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