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- PDB-7shg: Polysaccharide ribofuranosyl transferase from Thermobacillus composti -

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Basic information

Entry
Database: PDB / ID: 7shg
TitlePolysaccharide ribofuranosyl transferase from Thermobacillus composti
ComponentsRibofuranosyl transferase
KeywordsTRANSFERASE / glycosyltransferase / phosphatase / ribofuranose
Function / homologyHAD superfamily / HAD-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesThermobacillus composti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKimber, M.S. / Kelly, S.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2020-07113 Canada
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: The biosynthetic origin of ribofuranose in bacterial polysaccharides.
Authors: Kelly, S.D. / Williams, D.M. / Nothof, J.T. / Kim, T. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.
History
DepositionOct 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribofuranosyl transferase
B: Ribofuranosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,9627
Polymers152,8182
Non-polymers1445
Water3,189177
1
A: Ribofuranosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4934
Polymers76,4091
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribofuranosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4693
Polymers76,4091
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 82.500, 234.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-856-

HOH

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Components

#1: Protein Ribofuranosyl transferase


Mass: 76409.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobacillus composti (bacteria) / Strain: DSM 18247 / JCM 13945 / KWC4 / Gene: Theco_3912 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: L0EJI9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.92 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 mM MgCl2, 10% PEG 20000, 100 mM Na HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9811 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 83914 / % possible obs: 90 % / Redundancy: 4.93 % / Biso Wilson estimate: 48.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.22
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 9187 / CC1/2: 0.675 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.5→49.16 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.5089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 2154 2.58 %
Rwork0.2511 81298 -
obs0.2522 83452 89.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9835 0 5 177 10017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002510056
X-RAY DIFFRACTIONf_angle_d0.487413550
X-RAY DIFFRACTIONf_chiral_restr0.04061467
X-RAY DIFFRACTIONf_plane_restr0.00341724
X-RAY DIFFRACTIONf_dihedral_angle_d14.66443757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.39861470.38785366X-RAY DIFFRACTION88.6
2.56-2.620.35251420.37885315X-RAY DIFFRACTION88.42
2.62-2.690.30871430.35395353X-RAY DIFFRACTION88.53
2.69-2.770.38261430.34995446X-RAY DIFFRACTION89.75
2.77-2.860.36591480.32645540X-RAY DIFFRACTION91.12
2.86-2.960.36271500.32945542X-RAY DIFFRACTION91.36
2.96-3.080.41351470.3185444X-RAY DIFFRACTION90.75
3.08-3.220.34471450.30255501X-RAY DIFFRACTION90.82
3.22-3.390.32751410.26355443X-RAY DIFFRACTION89.92
3.39-3.610.29661390.25115482X-RAY DIFFRACTION90.25
3.61-3.880.30051470.23295407X-RAY DIFFRACTION89.74
3.88-4.270.2771440.22025371X-RAY DIFFRACTION88.82
4.27-4.890.25141390.19035373X-RAY DIFFRACTION88.69
4.89-6.160.24611420.22055381X-RAY DIFFRACTION88.87
6.16-49.160.24181370.18835334X-RAY DIFFRACTION87.86
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)
13.182592466020.2869661918590.2012746917480.298701665536-0.7544328085412.105680541570.043815684090.1804789962510.107202890338-0.060776350726-0.121704804541-0.00784474842039-0.489180446922-0.7865773348849.92171611729E-50.542119088535-0.140099628389-0.03128803804160.7220381529060.05437791397120.50180128821449.44868.30523.207
21.433093068540.267551441888-0.3528757777970.635730345110.2207834349980.489925756606-0.2141824992040.2431307400380.432724158982-0.0801757687301-0.04597512228510.0138329286144-1.16790376094-0.240205265877-8.65871282977E-51.05286009551-0.102981238456-0.0842506287191.02780221461-0.01370309163650.68951593954453.83882.45624.568
32.710477467370.560130886127-0.2844332845430.876343343534-1.334286413542.54356624324-0.1847628905940.276551994367-0.187468774907-0.04251199200950.0678642459009-0.1774415109790.567849098297-0.6094400228866.97220472723E-50.517913897714-0.140530775625-0.01967768372530.678035434902-0.01022366306620.53704332636558.09859.55213.022
41.142855304780.543012174112-1.299039921091.65220055837-0.4813693965511.48847670679-0.1021551855930.2817769630010.113456698725-0.0733755644963-0.0769611060983-0.132398834184-0.101228143043-0.375696440608-5.074526159640.552969437752-0.0894653516934-0.04972453386750.7810838482680.03385204734250.5123349216256.62667.2634.921
50.8301058391130.689507798217-1.21136049530.639309807778-1.070770171941.71276492034-0.3422593195390.5962041093050.150052160301-0.01142691668170.4272608202160.0478568072720.439929670317-0.886464644119-0.0002565506124940.54015855053-0.20412530597-0.01105811797930.842257505346-0.04750586605590.56623234609840.38959.19119.822
62.673248860640.884721009140.7302966359890.7236131262881.123722903531.943048715220.0175246734632-0.0703530529177-0.088178796132-0.00225264920078-0.1077250766430.1100616078040.00573649658109-0.220964773319-2.876729213570.517924817174-0.109395284674-0.009090951985920.7565828015470.01489215268210.52128727966553.50756.53548.838
71.4326936826-0.07826197995061.264774625610.2383209494870.2270450141171.28573442043-0.148424613287-0.1338364970230.05032330937810.211450553732-0.04677797341460.07473525333240.1041146225020.280147976767-4.07285647828E-50.605542032351-0.14336046651-0.002931416956990.7838144086540.04293682942760.52346739192764.24961.13463.896
81.319040452860.188966980807-0.01566297991882.206288483910.2951454973561.237825437620.05804425475330.138509235881-0.2733554324760.586358775588-0.201915882352-0.09188214139870.5305504984570.0711613038956-6.5272744683E-60.827268381378-0.04525978709970.0016171079251.000971783640.04731293370880.57951858356672.32955.66585.062
90.697308672157-0.741911796369-0.1649297712252.594004287690.7509930775261.575240279770.02011431006680.05752283424920.120064560832-0.0264505839642-0.0140923883248-0.3051968713960.0653978065329-0.2368270853676.63653072401E-50.492443767723-0.2096713819420.01666507838950.7376156473680.01009650947420.52597971604270.18865.51661.471
103.199685334460.8954895932490.770948498880.733956051634-0.5573285801241.648572895360.410735570594-0.09245056788710.318569269670.362137503847-0.4784185014380.3292541245060.12794047745-0.204110764302-1.68454139818E-50.689666032276-0.02427120930510.01794099251040.747660621684-0.04912840736150.55565889683649.86763.45860.274
111.347595903910.890503365188-1.805593460021.42825326003-0.7544743386153.729659669470.375577111968-0.678285760375-0.5011827806930.154461322868-0.379052694467-0.2537199572891.008261507840.994570620835-0.2579492998590.7841610118460.006014450454910.04238554347240.0675504679399-0.01458263739650.67631686645364.2646.25656.113
122.40077440491-1.365096794020.7573829689682.21821112691-0.5116211696013.30465086256-0.272986146776-0.637047531757-0.1772780484160.2583026280380.4563318213360.118532894574-0.225653633513-1.068580586950.2314039491340.673495625554-0.191004872705-0.004156798725250.2381558672320.1082585102490.57987187803740.92452.29651.308
134.13085042008-0.009371929064150.8879332479270.2717563215940.3862268240283.06692839369-0.124212566814-0.7715728413840.2998511711150.1483656349490.0830457348750.046857002648-0.03288379753510.304841503206-0.1080999090590.334713765813-0.277504570642-0.0513447760036-0.318659058981-0.1094050340210.58658255124458.23768.305138.121
141.340880428660.649987242095-1.427617782691.18652612755-0.2792879253571.705705628590.06979771822170.3974067091340.131463672651-0.4435521729920.1847594406-0.108017231071-0.950104564072-0.6792234945950.03186952474670.88583057628-0.1611035343870.06623891869910.0780705245590.006920594508790.61206456616854.14182.504136.899
152.337039469840.217520506707-0.01231618527681.51914923320.5567398737132.43091687595-0.109186064981-0.401479129535-0.2747236248510.1452167315210.1884091542530.03909042670530.3277584059110.0623179383863-1.83649793269E-50.52417619634-0.0943504642434-0.02174513110910.7767045138950.009582487077770.53774178895249.56959.62148.254
162.148575468820.0671242073774-1.521482656282.82818924360.9845273633493.11732183487-0.183437326568-0.3825455657490.242819845625-0.01008933170810.03652863569420.064442575053-0.09106875265760.101751278587-0.000134576237820.489236579129-0.138701554796-0.02203695842540.70411356795-0.01182430440160.50367309123450.97667.341156.386
171.9878728911-0.696780178722-1.742267567880.1231743670390.6217772812191.64457139108-0.13794737343-0.30008396276-0.1889225744630.08225348290670.144859000189-0.07477605218510.05286661533471.02393012836-0.0002762042547340.572911820858-0.08590910269050.02381046566960.8120917901510.04926945371490.57352042906967.25959.33141.448
184.00103344869-1.83951755549-0.2416944789731.0792866961-0.241252523842.880502343510.109260446535-0.00852858011011-0.0654877160041-0.333099607974-0.0173415106083-0.0562881755756-0.15288544410.0648912744926-1.30815710681E-50.523853556626-0.251856592707-0.01626688747320.4351017162790.01517894785090.49592328521854.15356.626112.286
190.9917770298740.02397915857270.4892762832120.307484381406-0.4734105804860.993750977811-0.06298323381040.272878309783-0.0139603497396-0.198191166956-0.167853706178-0.1455084429710.0390184407427-0.406080060266-0.0003226230060.676510631803-0.08619202459360.05302784072720.812348591432-0.002071930445140.55813202829343.46561.00897.307
201.642150883770.516979701011-0.08543638032751.11231832632-0.1993951220880.905421517736-0.1584476809070.279879569025-0.223692864494-0.7323616061420.0563020826040.008659768872820.569557368837-0.492700810723-0.0001125837774150.886602989691-0.218548844498-0.04843652442471.12821257217-0.02062806555460.63507231007735.66355.29276.071
212.26606478441-0.1294581175030.7707776454352.57538451823-1.19976801812.061398815730.05751443716410.4933706097580.113114637825-0.0163831528801-0.06979176349050.274092243214-0.246203103322-0.3493412246046.73858797822E-50.625609472394-0.114539671090.02786992514060.886443561463-0.04546736441820.52911276037437.31465.26799.64
221.78899156186-0.931854970440.8605434543470.791806756563-0.8727246142081.959747895-0.1315669484440.105041515650.00867058152179-0.06120075412640.1913301351140.0100177623822-0.00539049397510.263763663442-9.129048829020.612424610612-0.177335799337-0.02405306598650.7058670799-0.04243831568390.52619487533157.66963.489100.763
232.34498201425-0.9302533763370.9170415780771.169397878990.3848654037540.8951633178710.2993874491060.492680283754-0.5171147180080.00167310870339-0.05088501200810.211322230580.49520738687-0.522065989185-0.0006578621664280.793404938935-0.2804768690420.09930055116720.86944148055-0.04213162732440.71113516165143.55146.198104.889
242.636001825670.202959614513-0.8739117132371.4907013221-1.752501341972.21760196791-0.09427070257160.105524030487-0.37038077643-0.307233490738-0.0813094267741-0.05638046299260.5061436069550.557799703447-5.15809859953E-50.64588932784-0.09781727071780.04069870204820.911248042909-0.1097252650410.53860668390366.85452.435109.846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:58 )A9 - 58
2X-RAY DIFFRACTION2( CHAIN A AND RESID 59:108 )A59 - 108
3X-RAY DIFFRACTION3( CHAIN A AND RESID 109:158 )A109 - 158
4X-RAY DIFFRACTION4( CHAIN A AND RESID 159:208 )A159 - 208
5X-RAY DIFFRACTION5( CHAIN A AND RESID 209:258 )A209 - 258
6X-RAY DIFFRACTION6( CHAIN A AND RESID 259:308 )A259 - 308
7X-RAY DIFFRACTION7( CHAIN A AND RESID 309:358 )A309 - 358
8X-RAY DIFFRACTION8( CHAIN A AND RESID 359:408 )A359 - 408
9X-RAY DIFFRACTION9( CHAIN A AND RESID 409:458 )A409 - 458
10X-RAY DIFFRACTION10( CHAIN A AND RESID 459:508 )A459 - 508
11X-RAY DIFFRACTION11( CHAIN A AND RESID 509:558 )A509 - 558
12X-RAY DIFFRACTION12( CHAIN A AND RESID 559:597 )A559 - 597
13X-RAY DIFFRACTION13( CHAIN B AND RESID 9:58 )B9 - 58
14X-RAY DIFFRACTION14( CHAIN B AND RESID 59:108 )B59 - 108
15X-RAY DIFFRACTION15( CHAIN B AND RESID 109:158 )B109 - 158
16X-RAY DIFFRACTION16( CHAIN B AND RESID 159:208 )B159 - 208
17X-RAY DIFFRACTION17( CHAIN B AND RESID 209:258 )B209 - 258
18X-RAY DIFFRACTION18( CHAIN B AND RESID 259:308 )B259 - 308
19X-RAY DIFFRACTION19( CHAIN B AND RESID 309:358 )B309 - 358
20X-RAY DIFFRACTION20( CHAIN B AND RESID 359:408 )B359 - 408
21X-RAY DIFFRACTION21( CHAIN B AND RESID 409:458 )B409 - 458
22X-RAY DIFFRACTION22( CHAIN B AND RESID 459:508 )B459 - 508
23X-RAY DIFFRACTION23( CHAIN B AND RESID 509:558 )B509 - 558
24X-RAY DIFFRACTION24( CHAIN B AND RESID 559:597 )B559 - 597

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