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- PDB-8bz7: Crystal structure of the L. monocytogenes RmlT in complex with TD... -

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Basic information

Entry
Database: PDB / ID: 8bz7
TitleCrystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / D(-)-TARTARIC ACID / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Glycosyltransferase
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 TDP-rhamnose
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)434,86035
Polymers429,8286
Non-polymers5,03329
Water21,4921193
1
A: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,05713
Polymers143,2762
Non-polymers1,78111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-48 kcal/mol
Surface area51800 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules

C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,93011
Polymers143,2762
Non-polymers1,6549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5190 Å2
ΔGint-41 kcal/mol
Surface area52030 Å2
MethodPISA
3
E: Glycosyltransferase
hetero molecules

F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,87311
Polymers143,2762
Non-polymers1,5979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5000 Å2
ΔGint-46 kcal/mol
Surface area52180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.988, 291.265, 92.394
Angle α, β, γ (deg.)90.000, 100.379, 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 , 6 types, 1222 molecules

#2: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H26N2O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1193 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7.0 0.2 M Potassium sodium 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: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 227206 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 46.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.069 / Rsym value: 0.059 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.087 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 11233 / CC1/2: 0.555 / Rpim(I) all: 0.658 / Rrim(I) all: 1.275 / Rsym value: 1.087

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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: 2.2→50 Å / SU ML: 0.2964 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 11129 4.9 %
Rwork0.1873 215982 -
obs0.1887 227111 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.86 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29172 0 317 1193 30682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004630144
X-RAY DIFFRACTIONf_angle_d0.670340757
X-RAY DIFFRACTIONf_chiral_restr0.28064466
X-RAY DIFFRACTIONf_plane_restr0.00465211
X-RAY DIFFRACTIONf_dihedral_angle_d24.262111382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.34183770.32217155X-RAY DIFFRACTION99.71
2.23-2.250.33213980.30797218X-RAY DIFFRACTION99.84
2.25-2.280.30613560.27967140X-RAY DIFFRACTION99.8
2.28-2.310.30023750.26837218X-RAY DIFFRACTION99.82
2.31-2.340.3193730.27547219X-RAY DIFFRACTION99.87
2.34-2.370.29283940.26227195X-RAY DIFFRACTION99.83
2.37-2.40.28443590.25977139X-RAY DIFFRACTION99.91
2.4-2.440.29333540.26557240X-RAY DIFFRACTION99.84
2.44-2.480.30883690.27927198X-RAY DIFFRACTION99.75
2.48-2.520.31223680.27737154X-RAY DIFFRACTION99.75
2.52-2.560.27893570.25047296X-RAY DIFFRACTION99.69
2.56-2.610.28373990.23857113X-RAY DIFFRACTION99.71
2.61-2.660.27053550.23177181X-RAY DIFFRACTION99.59
2.66-2.710.2843810.23357205X-RAY DIFFRACTION99.62
2.71-2.770.25133640.2217131X-RAY DIFFRACTION99.73
2.77-2.840.25533600.21967197X-RAY DIFFRACTION99.68
2.84-2.910.2554040.22427199X-RAY DIFFRACTION99.75
2.91-2.990.26433720.2387232X-RAY DIFFRACTION99.74
2.99-3.070.2793710.22417167X-RAY DIFFRACTION99.85
3.07-3.170.2483780.21377175X-RAY DIFFRACTION99.83
3.17-3.290.24063720.19517242X-RAY DIFFRACTION99.83
3.29-3.420.21113300.18567226X-RAY DIFFRACTION99.84
3.42-3.570.21094050.18227187X-RAY DIFFRACTION99.67
3.57-3.760.18273760.17097177X-RAY DIFFRACTION99.79
3.76-40.16883540.15177241X-RAY DIFFRACTION99.71
4-4.310.17493400.14397253X-RAY DIFFRACTION99.83
4.31-4.740.14413540.12757218X-RAY DIFFRACTION99.68
4.74-5.420.15553500.13957266X-RAY DIFFRACTION99.62
5.42-6.830.19173870.1667180X-RAY DIFFRACTION99.7
6.83-500.17473970.1547220X-RAY DIFFRACTION99.05
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)
13.553361672910.506466756169-0.1838902702412.402618284390.2188312053232.553098619340.0768128454255-0.5179892179020.2449438690520.038795313069-0.2933206584220.8680639614440.215412833303-1.09618622490.1907704219240.360581975311-0.107074138-0.02984362878050.865890009121-0.2098590006160.6582438032253.5339394058-3.300317774395.55725904977
22.90246956953-0.1167008424351.160743495512.949102897080.6318910333251.575314039190.1824327924770.0622402240163-0.324417072782-0.25069120859-0.2214291085480.4583446771910.334364272813-0.4900801603040.01285706364040.382819034577-0.0922092092139-0.01096478739540.479616115927-0.07370805616080.37427311671917.1155235835-12.5454576541-3.49731900537
31.118360269990.1293792527140.4334544224212.291120910910.682482138611.37808970410.1815007819280.150299510436-0.238076449586-0.202197459757-0.0754331908512-0.05314383066220.3007563441330.0158438601754-0.1133826060610.3579404329380.01214308369080.009445702968880.342242224796-0.01338299076310.24096793771140.0640145395-9.678925947792.52227276351
42.09331386258-0.932850840822-0.800810013873.069769364112.195799661795.510661120490.132860139782-0.1955270881090.285673156353-0.101063447233-0.0179898954467-0.0919621440538-0.250259224532-0.0445298811056-0.1719818328530.232375444308-0.01598124029350.02477984421530.304415841494-0.01719669155930.44336755946532.787602400131.898946008523.5432102694
51.77606398340.5901707738070.007626947197063.07551090329-0.9314647494733.03946479098-0.1054980674750.5022453720930.257043512871-0.8671222142190.03614708082650.3951980586820.1906920477710.143576518640.06212848664630.471415148419-0.00928983610195-0.1148369183910.494406506510.07550049394220.4310901790310.723609952251.346741411313.7980012818
61.81307988031-0.3795686614740.1365085015053.53490112335-0.5399640485531.921791462240.03135685458170.0163145419790.610297115785-0.4288000502250.007919627340450.888697215883-0.144311177108-0.0980559713731-0.004348455300930.298131752318-0.00517860692947-0.09430245714010.3906193100350.04627290449580.7050622031283.5130295805958.780326869923.9305198279
70.647077190116-0.03525895602080.2672195821991.83036181801-0.1311473858760.705629287975-0.0712624647344-0.03682155134150.2859189359390.186343110045-0.02589827202570.285353753876-0.18081478405-0.09187633458490.1180634188730.271270156675-0.000222050195050.06152501136180.399150144517-0.04702165332540.514472716577.3450636264651.584793822746.968004103
85.01115622562-2.41491346339-0.7465524682124.426613432061.554105485683.24421261996-0.151004233792-0.0577469628642-0.1793923197820.110164489299-0.01049388053240.1948241231080.2877390594740.06407430521970.1744742569640.276822535628-0.06084472045780.0439729044460.287867205830.01383730388920.26354063941617.24831758377.3690845926631.0812833836
93.22111591677-1.361791498780.3580430306433.21192438723-0.01351807179281.79904355002-0.193452081592-0.3092386552270.318106938930.4926000169250.060775439338-0.677354650470.02744143592630.2899441090520.1057381596470.422747864129-0.00180233625387-0.06149720158930.4424283173790.01361676266040.37937096157771.476690537128.8044209144-15.9053559044
103.12801432297-0.5715195802130.7795403163832.36726536279-0.3790219044180.7468578547570.1640653527360.0465921128396-0.5577995609120.188925937899-0.0334804790656-0.0203173405930.2243113076230.181534579007-0.1095496957870.404425894690.04662075041070.04651077828440.4020695307640.03202698941350.34894920535957.866472644714.0196056829-21.8238625243
111.4119064985-0.4241240280160.3004338594821.509568089840.02214561375170.6420925970130.063728851435-0.228513475744-0.2320341081570.296791032546-0.03910737050350.2621107439040.119790550016-0.163685279956-0.01543064492010.424645992432-0.05872871314080.1106180686980.4634016965710.007636706945180.33459150078238.372780550232.549748988-22.1839994889
123.254683857632.3327856847-1.311007103113.99386245741-2.240749644163.477728751450.14715848249-0.01669624810650.4510092947920.300648737376-0.02538297480180.222063016998-0.2296225929090.0385875816027-0.140267487490.3744023962820.02735911988880.008515947689660.325530285821-0.08557032214220.49332781782354.769340299873.0305444088-24.7235691525
132.34988158023-0.8315883780890.3526878345164.19068833337-0.3141236794034.013830061330.073540678613-0.642974212431-0.4116999786830.7203660253180.1545581445730.4097419806680.822298692427-0.507841309123-0.2326638715930.872652902399-0.140458474827-0.002540553396840.6555774508160.1616808525530.43124634550558.239240471-11.635685610563.3428804479
142.09937442580.06487910357230.8386768718883.02933075074-0.2121668181233.860157089670.200005488441-0.207571995225-0.1298694611620.5480850231160.0496238642957-0.4565259824270.5969037538050.344216799131-0.2174493863560.4705563218730.0427830606877-0.1126017120920.4163006569440.004035492186560.36362189831669.5564367996-5.2962584178850.3151787551
151.071934568250.321675026110.4080738901441.860117117730.9695142489232.127899218210.1618607606820.057983514603-0.2761819276690.28699481054-0.0356531982146-0.04116996544090.6106157054160.0313649534715-0.07526493995040.3697215881630.0232735282944-0.03423816054780.333483601157-0.002949838050340.34594358622758.8508271422-9.9298292868827.1452613031
161.74061990499-0.01109249186410.04861588300382.57410630139-0.07943265821833.253905801390.07099203310930.5950164101340.193127098087-0.959241460238-0.3299547699860.0770488365525-0.230935481703-0.08510288651630.2641546838870.8518322096690.156021294745-0.1113466656790.5310555142880.03712341153960.39797637867.41905247978-59.22414802817.51980265327
170.882729766851-0.1675138684660.2712695868391.676441322430.5265160754491.86414645822-0.09302950441490.1348734352780.320777247162-0.416066964789-0.1962492447860.327052346735-0.689257934877-0.2102033178790.1952431565430.5879132936470.103812626062-0.1732038599180.357666031347-0.0186338399910.5091649066861.25937839313-49.538714844433.0926112885
186.65233148163-2.47887074798-0.224368942323.906928301260.5554906125572.34256873361-0.15762089975-0.0886762660224-0.2934714381830.1057833363190.05551836288920.1995449957420.1804033427010.1574571701230.1475903799510.4620126290680.01095796202960.04883914343240.29801725708-0.01790289223650.31830436880318.1225711794-94.606328268339.4046102028
192.73762101497-0.4297854651171.085106645812.50837583559-0.2281888200971.94506488938-0.258347848326-0.151627568570.6589685348210.4312990821080.121613458211-1.0366697571-0.2863276464130.5797400160630.07048956547240.521155709561-0.0262453301572-0.2368145538130.557185222181-0.1490287770240.91106270432462.1511396616-52.5943470826-15.0550572675
204.76207412727-0.4919199486281.876392332853.52835918954-1.615757717793.75070529107-0.191090874713-0.3739429648980.04260330538390.4788594807340.168953681289-0.8346794926890.04071316514970.2494246955320.002735269426790.472735061640.0483543472989-0.1795490084390.490117893018-0.124196330970.62383678738657.4346734659-61.7861524273-11.3454370392
212.541725263520.1232230968121.558460868472.231866207540.1914293372992.230571058860.50260385145-0.238038565621-0.9123968769170.3499482438970.0420567985808-0.4207780212550.6655042806150.0210413444976-0.4128687621870.519282569376-0.0156626529078-0.2123758128290.4299650143490.006175562744640.69048866217340.1943877492-74.4759199409-20.7427215458
221.921768189710.1162314865550.6953019576781.893156408290.1185023314162.10944846476-0.0098229741519-0.177581399450.1009205906550.116137795344-0.0484405776798-0.132758541537-0.246669146486-0.1798600997910.01098304269490.350826029140.0402407539833-0.02992157362210.318601247726-0.07588952527860.32455692237730.0699675883-51.0367789925-27.3269338692
231.463307494530.132710721263-0.4944622760110.0210133890908-0.09689136372251.426251140230.3171848157340.358337137460.751845762412-0.345198340393-0.152952258972-0.463150386021-0.8915956252940.148801688274-0.1749246014991.36033420458-0.06050208910290.01780664212280.5551449130640.08941971426251.041943447342.0095900029-16.5431890592-40.0264633433
240.531439664455-0.6299823164740.8667213953660.94338975121-0.9904486355431.380639622070.09309052030250.470464031180.670536632352-0.432594552017-0.175133571492-0.400759244079-0.9608647498240.216139213695-0.04546442201381.41996140244-0.1867346186080.07420900560350.5271568877760.1217163232741.0719011598443.5638284805-16.5695531995-41.1834206843
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 129 )AA18 - 1291 - 112
22chain 'A' and (resid 130 through 255 )AA130 - 255113 - 233
33chain 'A' and (resid 256 through 523 )AA256 - 523234 - 501
44chain 'A' and (resid 524 through 623 )AA524 - 623502 - 601
55chain 'B' and (resid 18 through 150 )BC18 - 1501 - 133
66chain 'B' and (resid 151 through 237 )BC151 - 237134 - 215
77chain 'B' and (resid 238 through 523 )BC238 - 523216 - 501
88chain 'B' and (resid 524 through 623 )BC524 - 623502 - 601
99chain 'C' and (resid 18 through 174 )CE18 - 1741 - 157
1010chain 'C' and (resid 175 through 303 )CE175 - 303158 - 280
1111chain 'C' and (resid 304 through 523 )CE304 - 523281 - 500
1212chain 'C' and (resid 524 through 623 )CE524 - 623501 - 600
1313chain 'D' and (resid 17 through 99 )DG17 - 991 - 83
1414chain 'D' and (resid 100 through 237 )DG100 - 23784 - 213
1515chain 'D' and (resid 238 through 623 )DG238 - 623214 - 599
1616chain 'E' and (resid 18 through 183 )EI18 - 1831 - 166
1717chain 'E' and (resid 184 through 523 )EI184 - 523167 - 498
1818chain 'E' and (resid 524 through 623 )EI524 - 623499 - 598
1919chain 'F' and (resid 18 through 174 )FK18 - 1741 - 157
2020chain 'F' and (resid 175 through 237 )FK175 - 237158 - 212
2121chain 'F' and (resid 238 through 354 )FK238 - 354213 - 329
2222chain 'F' and (resid 355 through 534 )FK355 - 534330 - 509
2323chain 'F' and (resid 535 through 575 )FK535 - 575510 - 550
2424chain 'F' and (resid 576 through 623 )FK576 - 623551 - 598

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