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- PDB-8dvz: Structure of the Campylobacter concisus glycosyltransferase PglA ... -

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Basic information

Entry
Database: PDB / ID: 8dvz
TitleStructure of the Campylobacter concisus glycosyltransferase PglA R282V variant
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: 2.27 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 30, 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)42,5922
Polymers41,9841
Non-polymers6071
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.971, 97.971, 100.768
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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


Mass: 41984.371 Da / Num. of mol.: 1 / Mutation: R282V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus (Campylobacter) / Strain: 33237 / 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.: 116 / 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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / Details: 10% 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: 24-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: 2.27→84.85 Å / Num. obs: 26101 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 45.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 3.9 % / Num. unique obs: 2337 / CC1/2: 0.813 / % possible all: 97.7

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Processing

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

6eji


Resolution: 2.27→64.9 Å / SU ML: 0.2918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 1364 5.24 %
Rwork0.199 24679 -
obs0.2005 26043 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 2.27→64.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 39 116 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332976
X-RAY DIFFRACTIONf_angle_d0.73514013
X-RAY DIFFRACTIONf_chiral_restr0.0446452
X-RAY DIFFRACTIONf_plane_restr0.0037506
X-RAY DIFFRACTIONf_dihedral_angle_d6.1921399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.350.33021380.2962373X-RAY DIFFRACTION97.44
2.35-2.440.29111540.26072394X-RAY DIFFRACTION97.92
2.44-2.550.29561300.23572448X-RAY DIFFRACTION99.31
2.55-2.690.28421430.21712454X-RAY DIFFRACTION99.69
2.69-2.860.30091480.24672461X-RAY DIFFRACTION99.69
2.86-3.080.23541320.21752474X-RAY DIFFRACTION99.58
3.08-3.390.22761240.212489X-RAY DIFFRACTION99.24
3.39-3.880.21751330.18242473X-RAY DIFFRACTION98.27
3.88-4.880.20581250.16522528X-RAY DIFFRACTION99.21
4.89-64.90.19061370.18772585X-RAY DIFFRACTION98.05
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)
10.512271044063-0.006194990835830.1503525156011.467812550860.2437029358551.74289306146-0.0101233992048-0.3299373514170.09709464190760.007614528029340.03218090213460.1638825189190.0253881531996-0.253594889992-0.04084420844390.457808953082-0.100524103276-0.01601283012150.491792883404-0.0474857955910.42329094617434.8006951121-21.2909260279-3.21730173619
21.302649329250.4030735422450.02589481986271.678472733970.4255131245771.00325066613-0.0276018946579-0.0458128752166-0.05219695237180.06965052686240.0337091576315-0.024386497733-0.04240201595280.00654228890506-0.01329284386560.424140288269-0.0563845493223-0.02022141046380.3681121362610.02590107870930.33908450318630.3939445736-37.3729111989-17.5247377093
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 123 )2 - 1231 - 122
22chain 'A' and (resid 124 through 371 )124 - 371123 - 370

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