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- PDB-5tyh: PglD from Campylobacter jejuni NCTC 11168 in complex with 5-(2-fu... -

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Basic information

Entry
Database: PDB / ID: 5tyh
TitlePglD from Campylobacter jejuni NCTC 11168 in complex with 5-(2-furanyl)-1H-pyrazole-3-carboxylic acid
ComponentsUDP-N-acetylbacillosamine N-acetyltransferase
Keywordstransferase/transferase inhibitor / Acetyltransferase Bacterial N-glycan biosynthesis Inhibitor Fragment-based discovery / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


UDP-N-acetylbacillosamine N-acetyltransferase / protein N-linked glycosylation via asparagine / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-(furan-2-yl)-1H-pyrazole-5-carboxylic acid / UDP-N-acetylbacillosamine N-acetyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorrison, J.P. / Imperiali, B.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni.
Authors: De Schutter, J.W. / Morrison, J.P. / Morrison, M.J. / Ciulli, A. / Imperiali, B.
History
DepositionNov 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7463
Polymers21,3901
Non-polymers3562
Water1,33374
1
A: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules

A: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules

A: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2399
Polymers64,1703
Non-polymers1,0696
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6810 Å2
ΔGint-45 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.726, 86.726, 65.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein UDP-N-acetylbacillosamine N-acetyltransferase / Protein glycosylation D / UDP-4-amino-4 / 6-dideoxy-N-acetyl-alpha-D-glucosamine N-acetyltransferase


Mass: 21389.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: pglD, Cj1123c / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)
References: UniProt: Q0P9D1, UDP-N-acetylbacillosamine N-acetyltransferase
#2: Chemical ChemComp-7O4 / 3-(furan-2-yl)-1H-pyrazole-5-carboxylic acid


Mass: 178.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.5, 0.1 mM sodium acetate, 1.9 M ammonium sulphate, 22 C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16473 / % possible obs: 97.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.3
Reflection shellResolution: 2.102→2.155 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.3 / % possible all: 83.11

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOLREPphasing
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NPO

2npo


Resolution: 2.1→12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.58 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 810 5 %RANDOM
Rwork0.196 ---
obs0.19823 15234 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 45.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 26 74 1484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9861927
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63725.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67815253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.832153
X-RAY DIFFRACTIONr_chiral_restr0.1320.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211041
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9931.5908
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93721455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1883524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4244.5472
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 56 -
Rwork0.293 923 -
obs--83.11 %

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