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- PDB-9gzj: Crystal structure of the L. monocytogenes RmlT in complex with 3-... -

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Basic information

Entry
Database: PDB / ID: 9gzj
TitleCrystal structure of the L. monocytogenes RmlT in complex with 3-RboP-(CH2)6NH2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homology
Function and homology information


Transferases; Glycosyltransferases / glycosyltransferase activity / 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
: / Glycosyltransferase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
DepositionOct 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,81210
Polymers143,2762
Non-polymers2,5368
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-24 kcal/mol
Surface area52760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.248, 103.386, 178.560
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: 71637.930 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-A1IRZ / (Ribitol-phosphate)3-(CH2)6-NH2 / [(2S,3S,4R)-5-[[(2S,3R,4R)-5-[6-azanylhexoxy(oxidanyl)phosphoryl]oxy-2,3,4-tris(oxidanyl)pentoxy]-oxidanyl-phosphoryl]oxy-2,3,4-tris(oxidanyl)pentyl] [(2R,3S,4S)-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate


Mass: 759.521 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H48NO22P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5 0.15 M K/Na tartrate tetrahydrate 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.34→48.42 Å / Num. obs: 66054 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Rsym value: 0.079 / Net I/σ(I): 16.2
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4341 / CC1/2: 0.598 / Rpim(I) all: 0.601 / Rrim(I) all: 1.492 / Rsym value: 1.363 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→41.62 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 3244 4.92 %
Rwork0.1923 62706 -
obs0.194 65950 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.93 Å2
Refinement stepCycle: LAST / Resolution: 2.34→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 91 282 9957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00339867
X-RAY DIFFRACTIONf_angle_d0.552113324
X-RAY DIFFRACTIONf_chiral_restr0.0461457
X-RAY DIFFRACTIONf_plane_restr0.00381696
X-RAY DIFFRACTIONf_dihedral_angle_d12.59983691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.34711430.32082667X-RAY DIFFRACTION97.94
2.37-2.410.30121480.29452650X-RAY DIFFRACTION99.96
2.41-2.450.29481380.27192711X-RAY DIFFRACTION99.96
2.45-2.490.30961290.26962675X-RAY DIFFRACTION100
2.49-2.530.31571680.26732683X-RAY DIFFRACTION99.96
2.53-2.580.29771330.27162717X-RAY DIFFRACTION99.96
2.58-2.640.31891380.27172674X-RAY DIFFRACTION99.89
2.64-2.690.28731340.2582722X-RAY DIFFRACTION100
2.69-2.760.28411250.23822725X-RAY DIFFRACTION100
2.76-2.830.27821280.22122715X-RAY DIFFRACTION100
2.83-2.90.22921430.22542708X-RAY DIFFRACTION99.93
2.9-2.990.26351260.2262728X-RAY DIFFRACTION100
2.99-3.080.26731460.2262736X-RAY DIFFRACTION99.9
3.08-3.190.25951420.24022683X-RAY DIFFRACTION99.96
3.19-3.320.29521560.21632747X-RAY DIFFRACTION100
3.32-3.470.24291320.19522713X-RAY DIFFRACTION99.96
3.47-3.660.22941420.19022727X-RAY DIFFRACTION100
3.66-3.880.19631340.17672737X-RAY DIFFRACTION99.9
3.88-4.180.19131380.15932765X-RAY DIFFRACTION99.97
4.18-4.60.19191280.14452772X-RAY DIFFRACTION100
4.6-5.270.16791680.14942753X-RAY DIFFRACTION99.97
5.27-6.630.22041530.18282813X-RAY DIFFRACTION99.97
6.64-41.620.19011520.16662885X-RAY DIFFRACTION98.03
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)
14.442994201990.0991043390562-1.313059750971.506284875150.3659166703571.955357672650.05688858023070.0377208222168-0.1411952365620.0800432155267-0.03437224042030.1484727640820.0552832777715-0.190180597243-0.02398226844720.342109720127-0.0232313235596-0.0134847176920.267280853918-0.003781432282580.367731520779-28.996126922620.1124609935-6.62303292474
21.27146826484-0.352053820341-0.2492517209165.7939135574-1.665476131351.771141933420.02870134607680.01725406767480.1106452238820.0315207503723-0.01884999359640.291710297796-0.244744892854-0.142627516458-0.0442348903920.258943099437-0.001416560991470.00492025079360.307620987433-0.03801242062120.358117660348-22.319919769732.8093588169-11.6696760104
30.9300372914780.4336754410850.1847549958591.60657396480.4807467170351.01064727963-0.01902175646260.397464743993-0.258364193082-0.2359530868920.0620090614676-0.2420226068560.07436855249790.0755729646755-0.0518508310850.344173294940.01741474232790.0414059006010.480313366291-0.1055029376560.394850456369-17.223483360113.7510698146-35.1714789249
43.46658920168-1.36301179778-1.837108111310.5681674544580.7355381920560.977593322753-0.8037657449240.3180895894411.42515703831-0.2675596740250.1289091198980.0281356178692-0.606633187906-0.8889239791510.5734006974541.262357856360.0850164396913-0.5085080312241.141257929630.1160123847411.06687382284-54.268916848829.2591855561-78.5410820075
52.17054453711-0.204533754229-0.9162916119860.9902779762151.217116381371.97089651937-0.01032513600471.123772211230.523392687086-0.323701719824-0.5124145981830.359164625588-1.104622175880.07652992740430.5560966092331.26384563799-0.165390580783-0.4391891074481.486190069230.2064397645341.05155299646-60.963502538923.3501044259-80.488483092
61.00259360034-0.8276408642381.704909246922.51132527507-0.4135211105225.06347813837-0.5333674111871.021075404040.281239535275-1.089560408250.5152789671280.630450082982-0.5847416534260.0233988044268-0.007435781600450.936086609651-0.362154575503-0.1953488604971.17779161180.2159365139680.691063119771-41.434415972117.7422746446-80.3817384329
71.490594303760.6173331232850.29120968041.761031145320.4878525086271.75474624469-0.2954050792280.6674112095960.0574320362754-0.4465090868290.503871646673-0.110156417152-0.5372089411370.35479611275-0.1832149574140.630060437225-0.153948542480.05103719570480.826163079872-0.03684808468480.426678672608-24.690131962923.5923935611-62.1588838433
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 167 )AA16 - 1671 - 152
22chain 'A' and (resid 168 through 255 )AA168 - 255153 - 240
33chain 'A' and (resid 256 through 623 )AA256 - 623241 - 608
44chain 'B' and (resid 19 through 55 )BD19 - 551 - 32
55chain 'B' and (resid 56 through 107 )BD56 - 10733 - 66
66chain 'B' and (resid 108 through 237 )BD108 - 23767 - 188
77chain 'B' and (resid 238 through 622 )BD238 - 622189 - 573

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