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- PDB-5t2y: Crystal Structure of C. jejuni PglD in complex with 5-methyl-4-(m... -

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Basic information

Entry
Database: PDB / ID: 5t2y
TitleCrystal Structure of C. jejuni PglD in complex with 5-methyl-4-(methylamino)-2-phenethylthieno[2,3-d]pyrimidine-6-carboxylic acid
ComponentsUDP-N-acetylbacillosamine N-acetyltransferase
Keywordstransferase/transferase inhibitor / Campylobacter jejuni bacterial acetyltransferase inhibitor complex / 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 / Rossmann fold ...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
Chem-753 / UDP-N-acetylbacillosamine N-acetyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å
AuthorsDe Schutter, J.W. / Imperiali, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM097241 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R03 MH096549 United States
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
DepositionAug 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: UDP-N-acetylbacillosamine N-acetyltransferase
B: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8679
Polymers42,7802
Non-polymers1,0877
Water6,503361
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)65,93915
Polymers64,1703
Non-polymers1,76912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area7560 Å2
ΔGint-36 kcal/mol
Surface area21220 Å2
MethodPISA
2
B: UDP-N-acetylbacillosamine N-acetyltransferase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)65,66312
Polymers64,1703
Non-polymers1,4939
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Buried area6710 Å2
ΔGint-39 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.696, 106.696, 46.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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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.: 2
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)
References: UniProt: Q0P9D1, UDP-N-acetylbacillosamine N-acetyltransferase
#2: Chemical ChemComp-753 / 5-methyl-4-(methylamino)-2-(2-phenylethyl)thieno[2,3-d]pyrimidine-6-carboxylic acid


Mass: 327.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N3O2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 15% PEG-3350 0.1M NaF 10% glycerol

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43477 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.9
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.68 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.94→21.198 Å / Cross valid method: NONE / σ(F): 1.96 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.1908 1632 3.75 %
Rwork0.1537 --
obs0.1563 43477 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→21.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 72 361 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073000
X-RAY DIFFRACTIONf_angle_d0.9584034
X-RAY DIFFRACTIONf_dihedral_angle_d12.6761808
X-RAY DIFFRACTIONf_chiral_restr0.071459
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9407-1.99780.26961340.22793477X-RAY DIFFRACTION95
1.9978-2.06220.2341360.2123479X-RAY DIFFRACTION94
2.0622-2.13580.21380.1913442X-RAY DIFFRACTION94
2.1358-2.22120.21581350.18363500X-RAY DIFFRACTION95
2.2212-2.32210.19331280.18113489X-RAY DIFFRACTION95
2.3221-2.44420.18061380.17323470X-RAY DIFFRACTION95
2.4442-2.5970.20711350.17043496X-RAY DIFFRACTION94
2.597-2.79690.2171280.16863473X-RAY DIFFRACTION95
2.7969-3.07720.21781460.14483528X-RAY DIFFRACTION95
3.0772-3.51980.19541300.13843465X-RAY DIFFRACTION95
3.5198-4.42450.16681420.11993505X-RAY DIFFRACTION95
4.4245-18.48110.17391410.13723481X-RAY DIFFRACTION95

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