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- PDB-6e66: Crystal structure of bacterial N-acetylglucosamine transferase NleB -

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Basic information

Entry
Database: PDB / ID: 6.0E+66
TitleCrystal structure of bacterial N-acetylglucosamine transferase NleB
ComponentsNleB
KeywordsTRANSFERASE / NleB / Bacterial effector / Arginine GlcNAcylation
Function / homology
Function and homology information


protein-arginine N-acetylglucosaminyltransferase activity / symbiont-mediated suppression of host programmed cell death / Transferases; Glycosyltransferases; Hexosyltransferases / manganese ion binding / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / extracellular region
Similarity search - Function
T3SS secreted effector NleB-like protein / Protein-arginine N-acetylglucosaminyltransferase NleB1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYao, Q. / Zheng, Y.Q. / Shao, F.
Citation
Journal: Mol.Cell / Year: 2019
Title: Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.
Authors: Ding, J. / Pan, X. / Du, L. / Yao, Q. / Xue, J. / Yao, H. / Wang, D.C. / Li, S. / Shao, F.
#1: Journal: Nature / Year: 2013
Title: Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains.
Authors: Li, S. / Zhang, L. / Yao, Q. / Li, L. / Dong, N. / Rong, J. / Gao, W. / Ding, X. / Sun, L. / Chen, X. / Chen, S. / Shao, F.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
A: NleB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2382
Polymers38,1761
Non-polymers621
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.587, 101.458, 38.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein NleB


Mass: 38175.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0NUY1, UniProt: B7UI21*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 ammonium sulfate, 0.1 M sodium cacodylate trihydrate at pH 6.5 and 30% PEG 8000

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 19964 / % possible obs: 97.94 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 21.4
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.439 / Num. unique obs: 1873

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Processing

Software
NameVersionClassification
PHENIX(dev_3120: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.744 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 24.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 998 5 %1996
Rwork0.2002 ---
obs0.2023 19963 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 4 84 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082311
X-RAY DIFFRACTIONf_angle_d1.053121
X-RAY DIFFRACTIONf_dihedral_angle_d3.581375
X-RAY DIFFRACTIONf_chiral_restr0.068329
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21060.31661340.23012561X-RAY DIFFRACTION94
2.2106-2.34890.28411390.22352625X-RAY DIFFRACTION97
2.3489-2.52990.29221400.21982662X-RAY DIFFRACTION98
2.5299-2.78390.29061420.23162692X-RAY DIFFRACTION98
2.7839-3.18530.25181430.22362734X-RAY DIFFRACTION99
3.1853-4.00760.23241460.18912775X-RAY DIFFRACTION100
4.0076-19.74510.19871540.17442916X-RAY DIFFRACTION100

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