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- PDB-8bz6: Crystal structure of the L. monocytogenes RmlT in complex with UD... -

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Basic information

Entry
Database: PDB / ID: 8bz6
TitleCrystal structure of the L. monocytogenes RmlT in complex with UDP-glucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / ACETATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycosyltransferase
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCereija, T.B. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: To Be Published
Title: Crystal structure of the L. monocytogenes RmlT in complex with UDP-glucose
Authors: Monteiro, R. / Cereija, T.B. / Morais-Cabral, J.H. / Cabanes, D.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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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)435,39153
Polymers429,8286
Non-polymers5,56347
Water12,142674
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,14218
Polymers143,2762
Non-polymers1,86616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,16618
Polymers143,2762
Non-polymers1,89016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glycosyltransferase
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,08317
Polymers143,2762
Non-polymers1,80715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.523, 291.057, 89.824
Angle α, β, γ (deg.)90.000, 100.079, 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

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 721 molecules

#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.5 0.2 M Sodium acetate 15% (w/v) PEG 4,000

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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: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.4→49.34 Å / Num. obs: 166303 / % possible obs: 99.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 56.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Rrim(I) all: 0.111 / Rsym value: 0.103 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8154 / CC1/2: 0.62 / Rpim(I) all: 0.615 / Rrim(I) all: 1.678 / Rsym value: 1.56 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BZ4
Resolution: 2.4→44.22 Å / SU ML: 0.3525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 8373 5.04 %
Rwork0.1948 157880 -
obs0.1968 166253 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.55 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29427 0 356 674 30457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004230397
X-RAY DIFFRACTIONf_angle_d0.580941075
X-RAY DIFFRACTIONf_chiral_restr0.23174490
X-RAY DIFFRACTIONf_plane_restr0.00455281
X-RAY DIFFRACTIONf_dihedral_angle_d22.196811431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.36422480.33815200X-RAY DIFFRACTION97.34
2.43-2.460.35112710.29375207X-RAY DIFFRACTION98.45
2.46-2.490.37122650.28785241X-RAY DIFFRACTION98.46
2.49-2.520.32662740.2725205X-RAY DIFFRACTION98.7
2.52-2.550.29173130.26545194X-RAY DIFFRACTION98.67
2.55-2.590.31832610.26585284X-RAY DIFFRACTION98.79
2.59-2.620.30642670.26755230X-RAY DIFFRACTION98.67
2.62-2.660.31252730.27095224X-RAY DIFFRACTION98.83
2.66-2.70.34412620.28995242X-RAY DIFFRACTION98.83
2.7-2.750.37882800.32985299X-RAY DIFFRACTION98.92
2.75-2.790.33882610.28455256X-RAY DIFFRACTION98.92
2.79-2.850.32122520.27375252X-RAY DIFFRACTION99.03
2.85-2.90.32652970.25775247X-RAY DIFFRACTION99.11
2.9-2.960.27343080.23715213X-RAY DIFFRACTION99.1
2.96-3.020.2982710.22975259X-RAY DIFFRACTION99.1
3.02-3.090.26552880.22185267X-RAY DIFFRACTION99.16
3.09-3.170.25772780.2255240X-RAY DIFFRACTION99.24
3.17-3.260.29082970.23325276X-RAY DIFFRACTION99.39
3.26-3.350.28762880.23075255X-RAY DIFFRACTION99.35
3.35-3.460.26112570.20535324X-RAY DIFFRACTION99.32
3.46-3.580.25082640.19375287X-RAY DIFFRACTION99.43
3.58-3.730.22042720.1855325X-RAY DIFFRACTION99.48
3.73-3.90.21962800.17825261X-RAY DIFFRACTION99.62
3.9-4.10.21922760.17485290X-RAY DIFFRACTION99.54
4.1-4.360.20142790.16025289X-RAY DIFFRACTION99.68
4.36-4.70.16433010.13975317X-RAY DIFFRACTION99.65
4.7-5.170.1822930.14715284X-RAY DIFFRACTION99.82
5.17-5.910.20413370.16465253X-RAY DIFFRACTION99.79
5.91-7.450.21172810.18375338X-RAY DIFFRACTION99.77
7.45-44.220.16872790.14195321X-RAY DIFFRACTION99.01
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)
13.806003009270.8101572862370.5143335408472.999001787380.3658208017152.842363153240.1175176628830.004715998738630.269361509222-0.0295278244281-0.2968703261910.7212801829250.055665964287-0.8114959237080.1466308356470.3850925825620.0495175938968-0.04381440394050.773750914656-0.1301641218350.5201262046577.1493978573-4.146668655282.32259319847
23.19046349878-0.04310388410341.442416548826.480677825750.917340080973.007617319480.100356759718-0.0699256449618-0.2472892912240.210623530048-0.1025525724620.5009351342930.538643860752-0.4326984376340.001694606168580.38270759011-0.03955824292180.01520191701070.669770276674-0.05805058293330.39407419991213.0892765448-13.92437117651.11191877823
31.017387603690.3378996795240.1430081792521.57295883040.4683869016511.056309522420.107654065290.240248418994-0.179780465573-0.143679676822-0.0133888790497-0.1532415810650.2275234786530.0167730740759-0.09487762755560.4085736637810.07213087127120.01818484010460.511741105363-0.02407462277190.32037670446137.3617633347-10.91392269562.29215878627
42.32783042168-1.2808721501-0.9097972829573.825436150332.947058561199.265225191940.079753161742-0.2569356133440.429398130432-0.1978877006210.00352627913313-0.324851395084-0.4612842513110.259687368053-0.08121858256340.279568358360.002041681090080.04826611576220.3832156391630.008056446641510.56837801870932.237009999732.323903852622.9112559741
51.27067011587-0.5623138248421.006615488032.994207907930.4812565046355.115017521390.202479498895-0.400636989456-0.3190893704570.8154776505430.00673703664527-0.1257382527281.201344612490.109642292092-0.1830511898190.8715509177440.0286060682893-0.1450286020950.6915688569560.03341512651480.50909380090764.7732400968-9.9859626623355.2000021188
63.14251074271.482711285162.470841303986.04736691955-1.007099858327.846704667860.298256963012-0.215725095255-0.1299651476380.9494188344560.188048598845-0.4373046231520.2787577541710.604169974312-0.4392395753890.5256339659720.0700483184585-0.1003522286730.649129071239-0.02253221953930.39915629606870.62248131170.81037801013452.7562986462
70.1888825798680.1681210739670.6049703149268.097971683910.01989484459163.324308639930.185158500214-0.401299559714-0.01761649973770.91366490527-0.1968533558780.589936057150.080220990499-0.4790643400230.007559603360280.612903668317-0.02204297679260.1123140742750.679593776539-0.0383831217960.43558421574858.30144767248.6347013010448.0465026005
81.557797913850.570570612370.8572756777782.58818749560.8454010284833.108160502220.1676115007530.135391373982-0.123478106323-0.00607469604629-0.0603966422662-0.2241330419070.2071791167740.347454798769-0.09937052215860.2387276069910.03198103821530.03076585945520.5187315759390.01331566459730.34936764462561.48375280691.0140298989825.1570145324
90.5659174138111.197584756170.4846848741494.48549982358-0.3648140903711.371154487160.518129623187-0.388056980337-0.9241109677870.0632793654541-0.3146969513750.09774800696981.88483951941-0.688053547074-0.1498351811231.9984192578-0.411088117249-0.3152281957550.8977263091750.1011187088711.1946375257150.4722747583-44.725574494225.7817654653
101.448446888290.904831025304-0.06681077191722.93443858822-1.177677655364.73685871912-0.1309086696690.4088397817710.192934496274-0.6551530225310.05725223785850.3684380943940.2142290487830.3106374888290.06080178828480.4770462769630.0228029646089-0.1197797623210.5204268671590.03641510955550.5481692324827.6900614882252.929815535614.9119922166
113.69083636002-1.259298005341.24147562582.69325364477-1.006677026595.28839809092-0.1573096683370.05552715606560.590345686926-0.433834399970.0557633407734-0.296701868115-0.6229690544680.5503838890430.054672696980.424066276573-0.0317108629117-0.01658089500350.5389322172820.03311839125650.6629372491498.6893051797660.643691153923.67878133
120.993045350660.1533928766480.1145723217593.84201620879-0.838133749431.43943535661-0.0173913843496-0.06194898424630.2813518115740.5771862793940.03702847709290.0863633486124-0.551509621914-0.0281891066015-0.007024808412350.4480547261640.02849205241090.08038856744750.462101979825-0.06158072543430.5725191545498.2116497851861.510255818346.3958031946
130.83546360729-0.700196103406-0.4641737347583.007737098111.075290002711.75477066519-0.01793599555280.004051706878570.000550103930863-0.00480720972616-0.0573556403880.25289203910.0184447915467-0.07639657102560.08320295388740.292321091952-0.01005929168560.03528143072470.428326285605-0.01290030738270.4089560235199.9964151816127.594263620339.5594350127
142.95956037633-1.419472618341.042966041462.877103348210.159630152551.23650960476-0.1037121333260.07288557082760.5444383844710.412884174816-0.236860565474-0.648340448542-0.2369682762810.5452179892060.2848645538270.496155442169-0.146757014703-0.06908852871080.6577071176950.1958174737140.5280059132254.419701061529.157285338374.6964154046
153.09191494216-1.080998609391.048432840045.89652861785-0.387811701080.546634713114-0.03032076472030.3506462754-0.0678999550867-0.00600098661089-0.178506153018-0.325770671338-0.1325761028950.3751154518170.1835353840950.497684170932-0.04808932171720.1123426742070.5447014397110.08119621329940.49503448763947.130415594221.05227277771.1162868943
160.6678911563450.0529836324979-0.09563100379591.43926830757-0.4126855010950.4109780759850.0659777018002-0.0154212917702-0.04069785112590.251208927576-0.1087872573650.0963855844277-0.0432776270889-0.004176050078350.04219319731020.479576325436-0.03989405068410.04432478219870.448245138285-0.02192504838940.36596490525727.49067398539.11889349666.4953909588
171.56871612651-0.25777622325-0.4399440721782.28438675899-0.3568364667973.073876927330.1539560706810.516721246322-0.0434108251457-0.931892507913-0.2627367269870.1691118023420.2702717549660.05275760409770.1195134053740.8835875821080.184389537202-0.1219442129850.547028974257-0.07953798143570.419759627278.53305370855-58.11019955355.8600714312
181.87356813167-0.0334773086274-0.6894330359924.82785217754-0.5648138448532.525999936090.1938424781130.2696075039430.380031561371-0.707242168809-0.1553496335490.0236185854151-0.159898330970.100807122079-0.03300463108580.6926609870380.110908257966-0.08182164825060.52600227864-0.03118202182720.4230907145437.36495639873-48.151694162111.391683419
190.78167368962-0.230096720560.2945720490332.27028769752-0.4216963295821.23863342174-0.0385276440561-0.0226414605350.1559418831-0.0371285045852-0.00783755880410.198164025096-0.368245356733-0.1399065246560.04789914970170.5289570839720.0667503514557-0.03124474866670.443172063388-0.0706582884590.4191592612331.98982340951-48.485982619134.5412458467
208.36709362923-2.60070015484-0.1761412690744.023830664420.4820445365531.67361805798-0.214321434635-0.235985684738-0.4132486687110.2963419982540.1203457524990.2475024895180.2903057827480.2051587622670.08903676699660.6082304557420.03059194273360.01998109056210.3456651751380.0005932300256040.32704486704418.3115430885-93.561872271237.6702113974
214.18359199092-0.3613168119151.565244003232.56635496378-0.3305384538572.23937394101-0.200615784567-0.1084420858050.570530036310.748699044968-0.129473206106-1.12382291287-0.3457084425890.6965899023660.2428715542930.773204801029-0.0888706149276-0.3796652738340.7117540511110.04147590593360.97269318071245.5869504041-53.341025786275.4774816777
223.547758573390.1090289052262.004733522395.987335622160.1057015390041.960607467910.100035302319-0.0649645482055-0.3649576733270.6603526105950.119440716277-0.9934909453390.1386119176670.258583030433-0.1653891710610.581456660554-0.0222697348202-0.1939502926720.5110853891050.01227907615760.73577814721437.5761554019-65.679176250373.037341789
231.45049614274-0.02355816831590.6392496635033.18823425091-0.3165968834582.24293801470.140626859191-0.210815303628-0.1943253818730.358554445847-0.100370483993-0.1906720566950.149355582995-0.141720774158-0.04434962418230.459173688515-0.044794220409-0.05504865500570.4407861918-0.03113357765290.3164741291316.6356692112-59.860701214164.4014892101
243.297153413831.64266737739-0.8012668011398.53232311372-2.750849326743.71205412170.1039474754150.3997205608410.655125145569-0.509899213802-0.0664334137629-0.387453973402-1.146266338850.329629036054-0.1208428253881.16350102625-0.110430092598-0.05998568717050.5397651315130.06819586909140.75871374231925.476668277-15.947813323349.4651319163
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 183 )AA18 - 1831 - 166
22chain 'A' and (resid 184 through 237 )AA184 - 237167 - 220
33chain 'A' and (resid 238 through 523 )AA238 - 523221 - 506
44chain 'A' and (resid 524 through 623 )AA524 - 623507 - 606
55chain 'B' and (resid 18 through 167 )BD18 - 1671 - 150
66chain 'B' and (resid 168 through 219 )BD168 - 219151 - 202
77chain 'B' and (resid 220 through 255 )BD220 - 255203 - 238
88chain 'B' and (resid 256 through 523 )BD256 - 523239 - 506
99chain 'B' and (resid 524 through 622 )BD524 - 622507 - 605
1010chain 'C' and (resid 18 through 183 )CF18 - 1831 - 166
1111chain 'C' and (resid 184 through 237 )CF184 - 237167 - 220
1212chain 'C' and (resid 238 through 385 )CF238 - 385221 - 368
1313chain 'C' and (resid 386 through 623 )CF386 - 623369 - 606
1414chain 'D' and (resid 18 through 183 )DI18 - 1831 - 166
1515chain 'D' and (resid 184 through 237 )DI184 - 237167 - 220
1616chain 'D' and (resid 238 through 623 )DI238 - 623221 - 606
1717chain 'E' and (resid 18 through 183 )EL18 - 1831 - 166
1818chain 'E' and (resid 184 through 237 )EL184 - 237167 - 220
1919chain 'E' and (resid 238 through 523 )EL238 - 523221 - 506
2020chain 'E' and (resid 524 through 623 )EL524 - 623507 - 606
2121chain 'F' and (resid 18 through 196 )FO18 - 1961 - 179
2222chain 'F' and (resid 197 through 255 )FO197 - 255180 - 238
2323chain 'F' and (resid 256 through 523 )FO256 - 523239 - 506
2424chain 'F' and (resid 524 through 623 )FO524 - 623507 - 606

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