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- PDB-9gzk: Crystal structure of the L. monocytogenes RmlT in complex with 4-... -

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Basic information

Entry
Database: PDB / ID: 9gzk
TitleCrystal structure of the L. monocytogenes RmlT in complex with 4-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: 2.52 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
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
C: Glycosyltransferase
D: Glycosyltransferase
E: Glycosyltransferase
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,78721
Polymers429,8286
Non-polymers7,95915
Water6,017334
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2457
Polymers143,2762
Non-polymers2,9705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-17 kcal/mol
Surface area52570 Å2
MethodPISA
2
C: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,2967
Polymers143,2762
Non-polymers2,0205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-26 kcal/mol
Surface area52140 Å2
MethodPISA
3
E: Glycosyltransferase
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2457
Polymers143,2762
Non-polymers2,9705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-17 kcal/mol
Surface area50870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.318, 290.759, 91.031
Angle α, β, γ (deg.)90.000, 100.245, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Glycosyltransferase


Mass: 71637.930 Da / Num. of mol.: 6
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-A1IR6 / (Ribitol-phosphate)4-(CH2)6-NH2 / [(2S,3S,4R)-5-[[(2S,3R,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)pentoxy]-oxidanyl-phosphoryl]oxy-2,3,4-tris(oxidanyl)pentyl] [(2R,3S,4S)-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate


Mass: 973.631 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H59NO29P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7.0 0.2 M K/Na tartrate tetrahydrate 17.5% (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 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.52→49 Å / Num. obs: 147299 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 60.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Rsym value: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 2.52→2.56 Å / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7280 / CC1/2: 0.516 / Rpim(I) all: 0.655 / Rrim(I) all: 1.242 / Rsym value: 1.053

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→42.89 Å / SU ML: 0.3835 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 7270 4.94 %
Rwork0.1985 139922 -
obs0.2002 147192 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.33 Å2
Refinement stepCycle: LAST / Resolution: 2.52→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28735 0 236 334 29305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001729595
X-RAY DIFFRACTIONf_angle_d0.423639980
X-RAY DIFFRACTIONf_chiral_restr0.04224364
X-RAY DIFFRACTIONf_plane_restr0.00285106
X-RAY DIFFRACTIONf_dihedral_angle_d11.775911069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.550.35072600.32794630X-RAY DIFFRACTION99.84
2.55-2.580.35332590.32054660X-RAY DIFFRACTION99.9
2.58-2.610.31892380.31424705X-RAY DIFFRACTION99.76
2.61-2.640.33552540.30864613X-RAY DIFFRACTION99.9
2.64-2.680.34182570.30774708X-RAY DIFFRACTION99.86
2.68-2.710.35012650.324639X-RAY DIFFRACTION99.92
2.71-2.750.37562600.32124649X-RAY DIFFRACTION99.86
2.75-2.790.3772320.30854677X-RAY DIFFRACTION99.86
2.79-2.840.33462540.29144689X-RAY DIFFRACTION99.7
2.84-2.880.31412390.27884653X-RAY DIFFRACTION99.94
2.88-2.930.29382520.26254670X-RAY DIFFRACTION99.78
2.93-2.990.29672760.2534651X-RAY DIFFRACTION99.8
2.99-3.050.30172300.25054680X-RAY DIFFRACTION99.76
3.05-3.110.29252410.24944693X-RAY DIFFRACTION99.86
3.11-3.170.2682510.25184654X-RAY DIFFRACTION99.67
3.17-3.250.26272360.23624691X-RAY DIFFRACTION99.72
3.25-3.330.26532390.22174673X-RAY DIFFRACTION99.72
3.33-3.420.26152240.21654677X-RAY DIFFRACTION99.47
3.42-3.520.28572290.21054654X-RAY DIFFRACTION99.31
3.52-3.630.24942250.20594696X-RAY DIFFRACTION99.53
3.63-3.760.21982510.20074697X-RAY DIFFRACTION99.52
3.76-3.910.21862390.17954652X-RAY DIFFRACTION99.41
3.91-4.090.21512630.17154608X-RAY DIFFRACTION99.23
4.09-4.310.16962300.16134685X-RAY DIFFRACTION99.45
4.31-4.580.17792290.1454712X-RAY DIFFRACTION99.32
4.58-4.930.1752140.14934618X-RAY DIFFRACTION98.57
4.93-5.430.18722350.15364714X-RAY DIFFRACTION99.44
5.43-6.210.2052440.17114655X-RAY DIFFRACTION99.13
6.21-7.810.22092110.18024679X-RAY DIFFRACTION98.59
7.82-42.890.16712330.15784540X-RAY DIFFRACTION95.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.53425692527-0.838450701785-0.483595756152.79132384095-0.3631556809392.90673598260.2425026357040.7305459455430.136781357178-0.919333930547-0.2506642438180.0254544326723-0.0532552349141-0.06590956764680.01282518422380.7518464633170.074573425589-0.07973323824490.5945973132170.03812321912030.3853854352087.875035618596.252651867756.17478487941
20.899379648859-0.409881982564-0.002256294247252.08212017153-0.1178620940661.32752163742-0.02364836817530.06009202116330.222349282305-0.0859814193356-0.05805297446750.104763823565-0.355311954605-0.1458666139080.08010983133090.4444412638130.0522543346391-0.03111621698420.462391308173-0.004857162069860.3718079406023.1218087686914.214700493634.0265866808
37.78697534833-3.106819912170.2591903579564.836045321870.9988686833471.91474169785-0.174178258327-0.142826290108-0.3033359382770.1037521927960.1457910365030.09962809346430.3180685124940.2064788140730.02567982340060.639266476984-0.003751578084970.08480031105450.353402808710.0208918873930.31053155205819.1267891885-30.856801163638.1149767239
43.136617815840.1316065972631.224446749152.82269327216-0.7698249462761.70002369468-0.335940439168-0.15911784230.3878699834660.536714691955-0.367628072682-1.94539316967-0.339619498060.8617371719980.5956063524980.894930227423-0.0937828696149-0.4624760075961.086751607080.3897868519511.7387365490450.623176246512.516300960874.3106326354
51.682009687280.2133970871520.5592848221092.11087442506-0.5257619972051.750083835390.170174212333-0.306973498248-0.4766094777520.518983849645-0.212712655087-0.8819451101420.2606092713030.322903577941-0.02789465986730.7567607785650.0690364550416-0.1984723985440.6490687688860.1393016385640.76102095063530.2929063538-4.2635786348172.5839497866
62.455695738681.753060011220.3823120849566.1198582189-1.096189529441.985647985190.0877529776138-0.209498326734-0.08884028462580.478605406282-0.129873116445-0.083451562113-0.0240825519113-0.06026956739010.05381080168160.4411355727470.0789862291183-0.02233772580140.441305755387-0.03923743844570.25034752449614.125266918110.908222599563.0835438156
73.222451039631.23068603993-1.290623389367.5872180191-4.215670838056.03988881095-0.1060905194360.4622647686960.570737346113-0.05395076567870.00828961300375-0.383857524787-0.2636489660260.5170108870720.02649426281760.774929414661-0.119336412044-0.2134203445010.5926970040460.05991900174230.73613456972525.688637949447.420652337649.8787134749
81.61472739827-0.383565518539-0.3250420313882.630048129550.5685338015394.04268097173-0.0128542252607-0.2871193009640.1290123644440.7306018907440.0756963607051-0.48142826017-0.088052967467-0.0720326388155-0.07540204487540.632184124455-0.0169888686023-0.09436262295260.5114288768280.07221758269570.65316813007961.6024901158-30.821823548374.3665115674
90.7038270727520.3745068008241.227542880454.40609189071-0.3286366238232.70296559561-0.00494008063159-0.1024550203850.06632319712220.396511240782-0.152019113423-0.423068339129-0.2775778807940.03730067701730.1559589285190.506385155118-0.01765904217460.04363540390630.5034723248390.03952161995190.78538761855965.5079142398-18.271249624962.2412585527
100.443013597082-0.04725996222390.304318386242.84889898951-0.04141313444730.8767032884580.01465856190640.04307823826790.113635636499-0.39413067234-0.0946493251575-0.424660396449-0.1676073000360.1499128635280.1006175303620.3908813728450.007896039772340.119903817580.4989315619760.0953900962590.67117414118463.4559370014-33.715151294540.436483506
118.318256278422.6882712067-3.127873127415.73779199544-1.855862413255.40146929294-0.2418167072670.194787388383-0.359242722766-0.012811222356-0.0418342111124-0.1909317581940.282088339515-0.2717688479740.2927182672830.3755508170370.0200309502047-0.0557323248330.3239603893330.01705285416460.3823549010153.7272579141-75.111134639157.9223377123
124.278609755011.81601796332-0.7069500283264.16668458462-0.7195598285842.29930326729-0.231877602205-0.135516064220.252346010813-0.3794417987780.4563224003270.5882423529690.144086490548-0.61153797721-0.232231872030.679521768837-0.00768530489876-0.1813793151070.768434365204-0.006283816358770.6157595385717.46741200462-52.267354241619.7114519716
133.525145916410.4875783616580.1695551307042.0588240509-0.7055916814680.361523944406-0.3525514355720.463140018695-0.332844265444-0.8776329384940.1159691860550.1582236644780.309335252357-0.4026003254340.2144693339351.07257524011-0.116489884730.01696227118930.650521837708-0.1421589079920.46365779364824.6608448368-53.58567127669.60117537757
143.19322610964-0.1520181230141.620881686123.19713932264-0.366891219591.361939399810.02472115337510.141585556345-0.945374876734-0.9344449993860.1899066951830.1590876549720.407908744377-0.265269370428-0.1527102434260.982776614303-0.1206806632930.1563505956450.53686846117-0.1164165998880.7220506152325.9717544057-66.743359274315.6755086498
152.5662114815-0.3424438071860.2341376006091.67019142185-0.172522829230.9476887721970.02700599746240.016991314977-0.737968466468-0.410768290447-0.0401140136671-0.1999692217270.3274124156970.1273513133490.001917869917030.6274866128260.07007821667020.1364082056120.4240469530.001931733091110.57656203591848.1088831477-52.375434250322.0311589562
164.16270332678-2.8065365797-2.287945949126.115819406432.509611721695.333209785430.1948489473550.1077667439180.507531837536-0.4196509552537.32103864754E-5-0.373735903893-0.0198863727267-0.0979618952363-0.2005075254790.434590856853-0.0315043018366-0.01403487811070.3794112213540.1182346180750.48422730686933.3358791059-8.8429682138623.539078792
173.34775467165-0.941214460374-0.8172601176282.928420758850.1948722067094.47081550678-0.223340126110.1867094056960.4814730802670.103570719741-0.140354271078-1.01787375544-0.04596449325861.021972902450.3094837145020.472381696155-0.119534370257-0.152835560750.8525843709310.3095775555481.0558721528567.9507634291-85.328989620483.133640069
182.655563690070.1445658144480.7152984094583.79713327431-1.258101703971.944883373570.00651449986969-0.121954027861-0.04613974776880.449307507287-0.287466195895-0.4960168988220.1771365353570.3875587171640.2270765081410.523439711640.0431162498695-0.01996655294310.4778200174770.06643900531680.39390889668550.4752795705-99.109980074191.698239708
191.22652094267-0.346735720687-0.02195800463663.22999693233-1.013266677141.282006918680.0598062512157-0.100611431146-0.06740296747060.402600495073-0.004793805009310.2309334441380.03030882834110.000208979404635-0.05464412329380.379188779436-0.04280321172610.02170570408570.424743230226-0.02570673069680.32208148850628.445241229-87.834163582586.232351304
202.383212085531.11844426527-0.3089560712944.45654234796-1.456268323785.34963994650.1511421700590.3821108734820.5080740208610.084786849904-0.0764673600678-0.0560988035577-0.4026427956430.0452766191341-0.09481936586870.3913602273440.02131287813640.00686397843140.4382990852250.1278239181810.76136551545438.2898416094-50.417058602765.5722528714
211.33685757931-0.215628862986-0.3186505486493.03517425848-0.9512109361341.11530592479-0.3007808648890.611434001061-0.0320171184363-2.030163916680.425525526359-0.3763851691950.3214156318590.407977674973-0.1087124408511.93051195632-0.08388389724140.05221145025881.89828844709-0.3878460845170.8016707079599.44139321766-95.708972515727.9050448833
220.447842454591-0.352713625421.559202176634.33376133079-0.5964874507133.547760608530.06695869192430.8901011063490.0387420658431-1.261131033480.0346790155720.2723946724620.386145497422-0.237963129033-0.06501419993170.749846163799-0.0773630450064-0.05801307108441.554210309340.02692453931150.6090732982062.09305327157-82.336578913740.9512180482
233.76638045469-0.07337378265581.007065398383.12136466211-0.346211698072.582385317750.05181453082140.570572590826-0.05610568512610.02776948444360.0164992772331-0.03493443571320.146184861022-0.10859062606-0.0651461525120.250942456586-0.03422394768270.02358941368550.640404759185-0.05735312788580.393162380088.62592722299-83.416286817365.6348460613
242.76461903471-2.46731743497-2.720585036784.725554435361.588090202122.930025828620.05343320505590.174392781678-0.9533773667420.05384499473590.269155428829-0.06220075555590.7079367009020.509738831666-0.3334711733930.9710642681220.0369299940064-0.152369238940.736997253321-0.3622513643812.0189167507812.5994870574-121.68682385170.3061896125
250.1277181265930.8427957859390.06224877946498.03753175127-0.3394061071410.3247875446190.4416875825490.2219592679450.187751423809-0.3480276637950.04546393307490.5697842732690.04362890439840.280966999878-0.5312514618290.9792183801530.12316397217-0.2057472039250.952986928429-0.5079247586991.7042367214215.2091524159-125.07176491263.5537740518
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 219 )AA17 - 2191 - 203
22chain 'A' and (resid 220 through 523 )AA220 - 523204 - 500
33chain 'A' and (resid 524 through 623 )AA524 - 623501 - 600
44chain 'B' and (resid 18 through 141 )BC18 - 1411 - 124
55chain 'B' and (resid 142 through 354 )BC142 - 354125 - 332
66chain 'B' and (resid 355 through 523 )BC355 - 523333 - 501
77chain 'B' and (resid 524 through 623 )BC524 - 623502 - 601
88chain 'C' and (resid 18 through 162 )CF18 - 1621 - 145
99chain 'C' and (resid 163 through 273 )CF163 - 273146 - 249
1010chain 'C' and (resid 274 through 523 )CF274 - 523250 - 499
1111chain 'C' and (resid 524 through 623 )CF524 - 623500 - 599
1212chain 'D' and (resid 18 through 99 )DH18 - 991 - 82
1313chain 'D' and (resid 100 through 174 )DH100 - 17483 - 157
1414chain 'D' and (resid 175 through 272 )DH175 - 272158 - 248
1515chain 'D' and (resid 273 through 523 )DH273 - 523249 - 499
1616chain 'D' and (resid 524 through 623 )DH524 - 623500 - 599
1717chain 'E' and (resid 18 through 128 )EJ18 - 1281 - 107
1818chain 'E' and (resid 129 through 304 )EJ129 - 304108 - 278
1919chain 'E' and (resid 305 through 523 )EJ305 - 523279 - 497
2020chain 'E' and (resid 524 through 623 )EJ524 - 623498 - 597
2121chain 'F' and (resid 18 through 90 )FL18 - 901 - 59
2222chain 'F' and (resid 91 through 286 )FL91 - 28660 - 248
2323chain 'F' and (resid 287 through 523 )FL287 - 523249 - 485
2424chain 'F' and (resid 524 through 560 )FL524 - 560486 - 512
2525chain 'F' and (resid 561 through 618 )FL561 - 618513 - 544

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