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- PDB-8dqd: Structure of the Campylobacter concisus glycosyltransferase PglA -

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Basic information

Entry
Database: PDB / ID: 8dqd
TitleStructure of the Campylobacter concisus glycosyltransferase PglA
ComponentsN, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
KeywordsMEMBRANE PROTEIN / glycosyltransferase / UDP-GalNAc
Function / homologyN,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase / N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase activity / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
Function and homology information
Biological speciesCampylobacter concisus (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsVuksanovic, N. / Clasman, J.R. / Bernstein, H.M. / Imperiali, B. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM039334 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA.
Authors: Vuksanovic, N. / Clasman, J.R. / Imperiali, B. / Allen, K.N.
History
DepositionJul 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6502
Polymers42,0421
Non-polymers6071
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.534, 96.534, 100.985
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase


Mass: 42042.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus (Campylobacter) / Gene: pglA, CCON33237_1464 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M4SVA9, N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 12% PEG 3350, 0.1 M sodium malonate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→83.6 Å / Num. obs: 51992 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 14.9
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2834 / CC1/2: 0.508 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EJI

6eji


Resolution: 1.78→64.4 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 2573 4.95 %
Rwork0.1729 49382 -
obs0.1741 51955 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.55 Å2
Refinement stepCycle: LAST / Resolution: 1.78→64.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 39 259 3186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922980
X-RAY DIFFRACTIONf_angle_d1.07764017
X-RAY DIFFRACTIONf_chiral_restr0.0607451
X-RAY DIFFRACTIONf_plane_restr0.0101507
X-RAY DIFFRACTIONf_dihedral_angle_d14.2561106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.37631310.33382612X-RAY DIFFRACTION95.21
1.82-1.850.34181650.28692668X-RAY DIFFRACTION98.78
1.85-1.890.27631390.25922724X-RAY DIFFRACTION98.89
1.89-1.940.28881490.23892674X-RAY DIFFRACTION98.74
1.94-1.990.27231390.23622709X-RAY DIFFRACTION98.89
1.99-2.040.26181170.21382709X-RAY DIFFRACTION98.5
2.04-2.10.22041400.18542760X-RAY DIFFRACTION99.11
2.1-2.170.23821180.15862712X-RAY DIFFRACTION99.16
2.17-2.240.19871680.15582751X-RAY DIFFRACTION99.35
2.24-2.330.18761350.14752723X-RAY DIFFRACTION99.69
2.33-2.440.19941550.16432716X-RAY DIFFRACTION99.55
2.44-2.570.17051690.15832745X-RAY DIFFRACTION99.69
2.57-2.730.18591400.18152772X-RAY DIFFRACTION99.76
2.73-2.940.2171340.1612756X-RAY DIFFRACTION99.18
2.94-3.240.19121450.1752787X-RAY DIFFRACTION99.9
3.24-3.70.19291450.15712800X-RAY DIFFRACTION99.86
3.71-4.670.14651370.15322836X-RAY DIFFRACTION99.97
4.67-64.40.20871470.18032928X-RAY DIFFRACTION99.48
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.48870487455-0.1232616336030.4535189320121.951682886510.5387805969941.87279434847-0.00562647281917-0.1569858199180.1551173881-0.05591379195480.07189602917540.127008255023-0.174384344947-0.116223371586-0.06425156493330.317595090134-0.06469133780820.003062690861810.303795537-0.01352481064830.34990858348133.815625537-20.5784699767-8.62612773504
22.658324154760.263967489193-0.1355714262952.82045917677-0.8894502337332.27652075775-0.0765399685552-0.121041202939-0.1195416095220.1818002420140.1116901156840.1460639850950.0346487984356-0.119153528129-0.0379620653750.320701019332-0.0644547296913-0.009422775600090.2958783525360.003523030911170.24990603269124.7971446235-44.5365416915-14.3626265667
30.55229367581-0.178329451971-0.0427006910161.995845445020.8917905933061.986170417530.03290029661740.0777264361832-0.0104599115579-0.06061055470570.0907194635308-0.1821335777020.06430013555330.188072324766-0.1254638752290.244051700886-0.06212747220440.03402916633790.2887895925310.005660589607370.22150596188336.9800086836-38.6876749396-22.1274688396
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 183 )2 - 1831 - 182
22chain 'A' and (resid 184 through 305 )184 - 305183 - 304
33chain 'A' and (resid 306 through 371 )306 - 371305 - 370

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