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- PDB-8qoy: Capsular polysaccharide synthesis multienzyme of Actinobacillus P... -

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Basic information

Entry
Database: PDB / ID: 8qoy
TitleCapsular polysaccharide synthesis multienzyme of Actinobacillus Pleuropneumoniae serotype 3
ComponentsTagF-like capsule polymerase Cps3D
KeywordsBIOSYNTHETIC PROTEIN / Bacterial protein
Function / homology
Function and homology information


CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / glycosyltransferase activity / plasma membrane
Similarity search - Function
CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats ...CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
TagF-like capsule polymerase Cps3D
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDi Domenico, V. / Litschko, C. / Schulze, J. / Bethe, A. / Cifuente, J.O. / Marina, A. / Budde, I. / Mast, T.A. / Sulewska, M. / Berger, M. ...Di Domenico, V. / Litschko, C. / Schulze, J. / Bethe, A. / Cifuente, J.O. / Marina, A. / Budde, I. / Mast, T.A. / Sulewska, M. / Berger, M. / Buettner, F. / Gerardy-Schahn, R. / Fiebig, T. / Guerin, M.E.
Funding support Spain, Germany, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2022-138694OB-I00 Spain
German Research Foundation (DFG)412824531 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Transition transferases prime bacterial capsule polymerization.
Authors: Litschko, C. / Di Domenico, V. / Schulze, J. / Li, S. / Ovchinnikova, O.G. / Voskuilen, T. / Bethe, A. / Cifuente, J.O. / Marina, A. / Budde, I. / Mast, T.A. / Sulewska, M. / Berger, M. / ...Authors: Litschko, C. / Di Domenico, V. / Schulze, J. / Li, S. / Ovchinnikova, O.G. / Voskuilen, T. / Bethe, A. / Cifuente, J.O. / Marina, A. / Budde, I. / Mast, T.A. / Sulewska, M. / Berger, M. / Buettner, F.F.R. / Lowary, T.L. / Whitfield, C. / Codee, J.D.C. / Schubert, M. / Guerin, M.E. / Fiebig, T.
History
DepositionSep 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TagF-like capsule polymerase Cps3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3934
Polymers134,1361
Non-polymers2583
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Physiological dimer confirmed with SEC experiment.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area46940 Å2
Unit cell
Length a, b, c (Å)207.911, 207.911, 93.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein TagF-like capsule polymerase Cps3D


Mass: 134135.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: cps3D / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S0ETM3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.83 Å3/Da / Density % sol: 74.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1.6 M magnesium sulphate heptahydrate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.67 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67 Å / Relative weight: 1
ReflectionResolution: 3→41.55 Å / Num. obs: 46791 / % possible obs: 99.86 % / Redundancy: 62.5 % / Biso Wilson estimate: 54.33 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 9.23
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 4630 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.55 Å / SU ML: 0.3766 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.1214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 2297 4.91 %
Rwork0.1826 44454 -
obs0.1845 46751 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.89 Å2
Refinement stepCycle: LAST / Resolution: 3→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8480 0 11 20 8511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028707
X-RAY DIFFRACTIONf_angle_d0.489411781
X-RAY DIFFRACTIONf_chiral_restr0.04111260
X-RAY DIFFRACTIONf_plane_restr0.0041517
X-RAY DIFFRACTIONf_dihedral_angle_d5.09311148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.28361580.27972714X-RAY DIFFRACTION99.97
3.07-3.140.32251550.25252748X-RAY DIFFRACTION99.83
3.14-3.210.33621300.25112776X-RAY DIFFRACTION99.97
3.21-3.30.29411220.2512792X-RAY DIFFRACTION99.93
3.3-3.40.28321580.23292709X-RAY DIFFRACTION99.93
3.4-3.510.2641540.20792764X-RAY DIFFRACTION99.9
3.51-3.630.26051440.20112752X-RAY DIFFRACTION99.97
3.63-3.780.23471480.1832751X-RAY DIFFRACTION99.9
3.78-3.950.23821660.17422734X-RAY DIFFRACTION99.93
3.95-4.160.1911390.16462785X-RAY DIFFRACTION99.97
4.16-4.420.15661280.14962794X-RAY DIFFRACTION100
4.42-4.760.17071270.14452804X-RAY DIFFRACTION100
4.76-5.240.19321230.15522810X-RAY DIFFRACTION100
5.24-5.990.21651570.17962793X-RAY DIFFRACTION100
5.99-7.540.20591230.18162842X-RAY DIFFRACTION100
7.55-41.550.16681650.14842886X-RAY DIFFRACTION99.38
Refinement TLS params.Method: refined / Origin x: -66.401205265 Å / Origin y: -55.359835971 Å / Origin z: 7.70951849694 Å
111213212223313233
T0.388299117015 Å20.0631679916384 Å20.0252859318659 Å2-0.466690774974 Å2-0.0108810878476 Å2--0.40587241979 Å2
L0.406661785631 °2-0.232046300253 °20.104926863865 °2-0.260247770459 °2-0.071539159408 °2--0.131927718212 °2
S-0.01297425348 Å °-0.0379577880898 Å °0.0822992441933 Å °0.0242818506002 Å °0.0288819919718 Å °-0.0309781348374 Å °-0.0369450463777 Å °0.016685646817 Å °0.00828706591665 Å °
Refinement TLS groupSelection details: all

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