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- PDB-6se1: Structure of Salmonella ser. Paratyphi A lipopolysaccharide acety... -

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Basic information

Entry
Database: PDB / ID: 6se1
TitleStructure of Salmonella ser. Paratyphi A lipopolysaccharide acetyltransferase periplasmic domain
ComponentsPutative lipopolysaccharide modification acyltransferase
KeywordsTRANSFERASE / SGNH / acetyltransferase / lipopolysaccharide
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / hydrolase activity, acting on ester bonds / acyltransferase activity, transferring groups other than amino-acyl groups / plasma membrane
Similarity search - Function
SGNH domain / SGNH domain (fused to AT3 domains) / : / Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Acyltransferase
Similarity search - Component
Biological speciesSalmonella paratyphi A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsTindall, S.N. / Pearson, C. / Herman, R. / Jenkins, H.T. / Thomas, G.H. / Potts, J.R. / Van der Woude, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Mbio / Year: 2020
Title: Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase.
Authors: Pearson, C.R. / Tindall, S.N. / Herman, R. / Jenkins, H.T. / Bateman, A. / Thomas, G.H. / Potts, J.R. / Van der Woude, M.W.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipopolysaccharide modification acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3094
Polymers29,0011
Non-polymers3083
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-16 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.740, 58.430, 90.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative lipopolysaccharide modification acyltransferase


Mass: 29000.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Periplasmic domain of OafB (residues 377-640) from Salmonella ser. Paratyphi A recombinantly expressed in E. coli Origami 2 cells from the pETFPP_2 vector.
Source: (gene. exp.) Salmonella paratyphi A (strain ATCC 9150 / SARB42) (bacteria)
Strain: ATCC 9150 / SARB42 / Gene: SPA0467 / Plasmid: pETFPP_2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: A0A0H2WM30
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM BisTris pH 5.5, 0.25 M Lithium sulfate, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.08→47.39 Å / Num. obs: 126378 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 12.2
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 6.4 % / Num. unique obs: 6232 / CC1/2: 0.651 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
Fragonphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: null

Resolution: 1.08→47.39 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.941 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 6379 5.051 %Random
Rwork0.1358 ---
all0.137 ---
obs-126289 99.919 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2---0.651 Å20 Å2
3---1.402 Å2
Refinement stepCycle: LAST / Resolution: 1.08→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 19 360 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171994
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6292983
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5694660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01323.564101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58715364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.775158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined0.210.2385
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.21642
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21039
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2169
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.24
X-RAY DIFFRACTIONr_nbd_other0.1810.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0840.226
X-RAY DIFFRACTIONr_mcbond_it0.9941.2091077
X-RAY DIFFRACTIONr_mcbond_other0.9881.2071076
X-RAY DIFFRACTIONr_mcangle_it1.4291.8211353
X-RAY DIFFRACTIONr_mcangle_other1.4321.8231354
X-RAY DIFFRACTIONr_scbond_it1.3881.4151101
X-RAY DIFFRACTIONr_scbond_other1.3871.4151102
X-RAY DIFFRACTIONr_scangle_it1.7492.0391613
X-RAY DIFFRACTIONr_scangle_other1.7482.0411614
X-RAY DIFFRACTIONr_lrange_it2.66816.1362486
X-RAY DIFFRACTIONr_lrange_other2.66916.1422487
X-RAY DIFFRACTIONr_rigid_bond_restr2.02934172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.08-1.1080.2964770.2787420.27192520.9220.92799.64330.268
1.108-1.1380.2354770.23885420.23890400.9490.94999.76770.23
1.138-1.1710.2264290.19883160.19987630.950.96699.79460.183
1.171-1.2070.1964540.18180560.18285120.9670.96999.97650.166
1.207-1.2470.174250.1778640.1782890.9680.971000.154
1.247-1.2910.1814120.15875730.15979870.9590.9799.9750.141
1.291-1.3390.1563760.1473630.14177390.9730.9751000.123
1.339-1.3940.1463320.12371420.12474750.9780.9899.98660.106
1.394-1.4560.1213570.11467510.11471080.9810.9821000.099
1.456-1.5270.1273660.10665000.10768660.9830.9861000.092
1.527-1.6090.1173400.09961660.165090.9860.98899.95390.088
1.609-1.7070.1212910.09958970.161880.9850.9871000.09
1.707-1.8250.122950.155300.10158260.9850.98799.98280.094
1.825-1.9710.1332680.10851760.1154440.9810.9841000.103
1.971-2.1580.1252400.1147770.11150190.9830.98699.96020.108
2.158-2.4120.1262220.1143110.1145390.9820.98599.86780.11
2.412-2.7840.1472130.12538530.12640660.9740.9791000.13
2.784-3.4070.151740.14532630.14534410.9760.97599.88380.155
3.407-4.8060.131440.13925800.13827300.9840.9899.78020.156
4.806-47.3920.215870.21115080.21115980.9640.96899.81230.237

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