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- PDB-8bz4: Crystal structure of the apo form of the L. monocytogenes RmlT -

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Basic information

Entry
Database: PDB / ID: 8bz4
TitleCrystal structure of the apo form of the L. monocytogenes RmlT
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


Transferases; Glycosyltransferases / hexosyltransferase activity / biosynthetic process / metal ion binding
Similarity search - Function
: / Glycosyl transferase TarS linker domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsCereija, T.B. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Nat Commun / Year: 2025
Title: Molecular properties of the RmlT wall teichoic acid rhamnosyltransferase that modulates virulence in Listeria monocytogenes.
Authors: Monteiro, R. / Cereija, T.B. / Pombinho, R. / Voskuilen, T. / Codee, J.D.C. / Sousa, S. / Morais-Cabral, J.H. / Cabanes, D.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,4373
Polymers144,4012
Non-polymers351
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-9 kcal/mol
Surface area54240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.427, 103.688, 178.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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 Glycosyltransferase


Mass: 72200.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: APD94_03445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A401AAP7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Succinic acid pH 7.0 10% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.52→49.78 Å / Num. obs: 53098 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 52.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.059 / Rrim(I) all: 0.218 / Rsym value: 0.21 / Net I/σ(I): 9.8
Reflection shellResolution: 2.52→2.6 Å / Rmerge(I) obs: 1.735 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4546 / CC1/2: 0.682 / Rpim(I) all: 0.491 / Rrim(I) all: 1.804 / Rsym value: 1.735

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
SHELXCDphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.52→49.78 Å / SU ML: 0.3564 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 2570 4.85 %
Rwork0.219 50441 -
obs0.2206 53011 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.95 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9597 0 1 241 9839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319802
X-RAY DIFFRACTIONf_angle_d0.52113237
X-RAY DIFFRACTIONf_chiral_restr0.71361444
X-RAY DIFFRACTIONf_plane_restr0.00371703
X-RAY DIFFRACTIONf_dihedral_angle_d21.14513678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.570.32441230.31432741X-RAY DIFFRACTION99.93
2.57-2.620.36271420.2942787X-RAY DIFFRACTION99.9
2.62-2.680.30611520.28862742X-RAY DIFFRACTION99.9
2.68-2.740.35011520.35512757X-RAY DIFFRACTION99.97
2.74-2.810.34391320.32082764X-RAY DIFFRACTION99.93
2.81-2.880.3341440.312804X-RAY DIFFRACTION100
2.88-2.970.27151270.27182780X-RAY DIFFRACTION100
2.97-3.070.32821340.25662771X-RAY DIFFRACTION100
3.07-3.170.28771490.25932776X-RAY DIFFRACTION99.97
3.18-3.30.31321400.27082769X-RAY DIFFRACTION99.97
3.3-3.450.26861380.25942814X-RAY DIFFRACTION100
3.45-3.630.27491530.21562777X-RAY DIFFRACTION99.9
3.63-3.860.24171500.19722787X-RAY DIFFRACTION100
3.86-4.160.21621560.18612827X-RAY DIFFRACTION100
4.16-4.580.21941300.16472828X-RAY DIFFRACTION100
4.58-5.240.19481350.15762841X-RAY DIFFRACTION100
5.24-6.60.21371480.1982879X-RAY DIFFRACTION99.97
6.6-49.780.22031650.1912997X-RAY DIFFRACTION99.87
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)
13.32143342587-0.0613272083657-1.10265020631.243468847620.2324943055821.66266208554-0.0554860495348-0.0373409280112-0.1467587624370.04524903863530.04039657345510.1397521459640.141792843236-0.1564024415790.01889950894240.3380275647-0.0443694006596-0.001898383935950.3079993026280.01842057848250.32435254749553.667855934919.9389324739171.966792685
21.292901984140.316706945044-0.1811628601292.34488093463-0.5636946987171.625789415370.00614863115110.05111246972630.126252386965-0.04432888321110.03342480420170.140408109058-0.156943876546-0.07059860153030.01545567263040.3017382750470.004447596532570.0005482032848820.330963037529-0.01726968002040.33909963773261.953788211532.4541521973166.927278235
30.8503027727760.5054886164570.2588946475681.800882019740.4166926406090.813472519882-0.05916349756920.316950706539-0.176856134352-0.2318293680030.111039119866-0.1582094895140.013591071690.130275983903-0.07384190579550.3201590226270.009589245896420.03346038633280.483852084048-0.06437609621280.36815688036566.155434354114.0411964362143.152679949
40.988472150747-0.266553692168-0.4744754895060.7284982642640.4012044291310.341681880073-0.8247283750450.125922033520.9708932821690.2318440650990.03101315895470.420986056944-0.794174550711-0.4202796429060.4026391121611.400726709320.119543097915-0.8035364799470.9713192537380.03342487203361.3801105337326.831864841227.4172034303100.857643214
51.433736917550.2376116321861.910199333572.138952146710.1502164705943.04924749527-0.9596163647590.6442780974261.04542809245-0.9160149956240.1675030088421.08656445029-0.611776806729-0.963046556810.3742324221041.27147318047-0.148854501987-0.7431768041111.213416876380.201183735941.5413607714428.930073968325.292715793397.6154300443
61.01772499242-0.007412032093461.806413160592.041214234760.4049692655283.49934138146-0.8445248106460.8361512535130.397347102704-1.190948265320.6617658201970.699062658843-0.6997787821110.2091383189210.1789756151511.01147935687-0.339801337394-0.2460596567171.113900554840.1536109191670.72544690202842.73242476415.648142518797.6574059231
71.582243804111.195899807410.6601843469811.965880310530.5573774378161.62527626709-0.1167073409210.641407974407-0.360950139434-0.3046052797890.468747266693-0.1074640082050.1548739611410.325255965228-0.1889888526570.483985058938-0.00619277034993-0.02101726894890.761925290608-0.2415633124420.54453963725952.25127880790.0102383200262110.965339615
81.74462803430.8464996599380.5611616646412.766745986080.8386834747661.9113371418-0.1937506046230.56555127314-0.0846445082244-0.5752480637490.379410956868-0.0819762049031-0.2733151725070.495777199062-0.2123061207340.505001588835-0.09909430962330.0485465841880.797346199619-0.07428217021230.3819257307465.167615204820.1418815531114.889321653
91.669478328410.7570130924370.1723077394093.194840283320.2706309879061.87822064693-0.123641473709-0.04891181770951.1950231547-0.4051959013570.1026767058470.348655592501-1.098725585960.0002237122215460.02523073009721.17929812407-0.00491361134287-0.01741403426690.5746966790010.0557234911941.1194589434155.409159753457.7703239626123.667422143
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 161 )AA18 - 1611 - 144
22chain 'A' and (resid 162 through 255 )AA162 - 255145 - 238
33chain 'A' and (resid 256 through 623 )AA256 - 623239 - 606
44chain 'B' and (resid 21 through 66 )BB21 - 661 - 37
55chain 'B' and (resid 67 through 128 )BB67 - 12838 - 90
66chain 'B' and (resid 129 through 237 )BB129 - 23791 - 191
77chain 'B' and (resid 238 through 354 )BB238 - 354192 - 308
88chain 'B' and (resid 355 through 512 )BB355 - 512309 - 466
99chain 'B' and (resid 513 through 623 )BB513 - 623467 - 577

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