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- PDB-8cse: WbbB in complex with alpha-Rha-(1-3)-beta-GlcNAc acceptor -

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Basic information

Entry
Database: PDB / ID: 8cse
TitleWbbB in complex with alpha-Rha-(1-3)-beta-GlcNAc acceptor
ComponentsN-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / Glycsoyltransferase / retaining / acceptor complex
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / CYTIDINE-5'-MONOPHOSPHATE / N-(8-hydroxyoctyl)-4-methoxybenzamide / Putative N-acetyl glucosaminyl transferase
Function and homology information
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsForrester, T.J.B. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: Nat Commun / Year: 2022
Title: The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Authors: Forrester, T.J.B. / Ovchinnikova, O.G. / Li, Z. / Kitova, E.N. / Nothof, J.T. / Koizumi, A. / Klassen, J.S. / Lowary, T.L. / Whitfield, C. / Kimber, M.S.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyl glucosaminyl transferase
B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,97814
Polymers92,1232
Non-polymers2,85412
Water5,495305
1
A: N-acetyl glucosaminyl transferase
hetero molecules

A: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,62516
Polymers92,1232
Non-polymers3,50114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: N-acetyl glucosaminyl transferase
hetero molecules

B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,33112
Polymers92,1232
Non-polymers2,20810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)92.380, 158.020, 117.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-747-

HOH

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Components

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Protein / Sugars , 2 types, 7 molecules AB

#1: Protein N-acetyl glucosaminyl transferase / retaining Kdo transferase


Mass: 46061.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wbbB / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U8B0
#2: Polysaccharide
alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2211m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 312 molecules

#3: Chemical ChemComp-PXV / N-(8-hydroxyoctyl)-4-methoxybenzamide


Mass: 279.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25NO3
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 100 mM HEPES, and 0.5 % Jeffamine ED-2001 5 mM CMP, 5mM acceptor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→37.76 Å / Num. obs: 38441 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.61 Å2 / Rsym value: 0.075 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.35 Å / Num. unique obs: 2366 / CC1/2: 0.792 / Rpim(I) all: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FA1

5fa1


Resolution: 2.3→37.76 Å / SU ML: 0.2744 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.468
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 1922 5 %
Rwork0.1674 36506 -
obs0.1702 38428 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 190 305 6765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01076662
X-RAY DIFFRACTIONf_angle_d1.10539065
X-RAY DIFFRACTIONf_chiral_restr0.05711031
X-RAY DIFFRACTIONf_plane_restr0.00831155
X-RAY DIFFRACTIONf_dihedral_angle_d16.14222355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31071350.23582579X-RAY DIFFRACTION99.89
2.36-2.420.28361360.22192568X-RAY DIFFRACTION99.78
2.42-2.490.27611360.22442587X-RAY DIFFRACTION99.71
2.49-2.570.29791360.21352584X-RAY DIFFRACTION99.93
2.57-2.660.28911350.20642569X-RAY DIFFRACTION99.85
2.66-2.770.27821380.19692613X-RAY DIFFRACTION99.89
2.77-2.90.24531350.19842570X-RAY DIFFRACTION99.74
2.9-3.050.26131380.18932618X-RAY DIFFRACTION99.89
3.05-3.240.25981360.17852593X-RAY DIFFRACTION99.93
3.24-3.490.21921370.15832594X-RAY DIFFRACTION99.82
3.49-3.840.20021380.14842634X-RAY DIFFRACTION99.82
3.84-4.40.19451390.13312639X-RAY DIFFRACTION99.78
4.4-5.540.19171390.13822641X-RAY DIFFRACTION99.75
5.54-37.760.19151440.16192717X-RAY DIFFRACTION97.98
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)
13.280780912690.79991413705-0.4937460854772.407787586420.79133347112.45931182190.100027967166-0.506324454932-0.5743205620790.677199437561-0.151216054242-0.1371203687190.5022066951220.184087717569-0.01975210110440.489710893037-0.010144877928-0.0244937239590.3539556711580.09253031412870.33996620553923.791211749727.942220121438.5999099725
20.5172160382370.8003804860740.486318434353.734460902512.454608379673.582168822780.0148698335620.07643721507070.0066473619488-0.089666232249-0.0315849889932-0.141759883755-0.06624233137980.194549069248-0.09925875074590.2337071624760.03608682267110.02451737856980.3067308781890.01982206615710.30855919122726.043698931734.456424932321.5305971367
33.2297018228-2.56931990341-0.01256783266982.825014403220.5242159180132.7200121738-0.1739408869040.571314778296-0.590638337387-0.621402143596-0.03828136897240.1555212676970.338609103055-0.404112030543-0.3559529877180.4990866755710.04701294138270.01259248205130.415994279141-0.09288834779020.34307822607917.957658519313.68750446816.59394463344
41.9376523043-2.098383048650.4178629582452.982375921580.8311829221463.93409808003-0.00643143065296-0.101473041223-0.3133199506210.00198878746723-0.05701760162680.3430248932010.185292158499-0.407439513246-0.1956306634060.280154068721-0.02534576709340.08420236962830.324782844391-0.01084342945690.385173731541.2970687061420.0605760720.4055312855
53.52825701752-0.4434976336590.2604384009793.096068250980.8377768772422.581029933490.2150669956780.4615315989620.354081298662-0.693190910658-0.149091131266-0.0521689974408-0.4198846391030.01318621860960.05611209415880.4741251816970.04938359303760.04812761492860.3528718633450.05658963014740.27854065973720.236095792464.250232382513.9452274916
61.25203727386-0.349962187410.04037082419974.280001464562.96581532513.323053210060.109458917117-0.07225818052310.133746803040.06232635769890.0463272752805-0.4550026944840.05555509027080.255718951855-0.01731418275280.24482043303-0.03364802386620.003665400292760.2928982719920.01224933464960.3812563898426.949740965957.663248120729.730126061
74.214822072892.97005552762-1.322882290642.21925991656-0.21507144532.996003632980.155031543524-0.5369344451450.4812495169670.170861171442-0.248152497009-0.0178309304322-0.136102503089-0.398623944763-0.4286544581070.484661686765-0.128794201368-0.03589445438980.596902830496-0.1623396430290.49921914441722.637366546278.87600432347.0264219853
82.574151901991.640273476320.261459185833.187657045250.8022677981685.440064082620.0189116857228-0.1389361609610.447960366010.0111794969787-0.02272737773830.275829842342-0.139385467192-0.365217974441-0.165069098010.2405935995270.00331328264556-0.02666367094650.3366743583340.0143586752470.4238362726493.7679738959172.197206205737.6389647602
93.01121070109-0.107259731171-0.3784619763931.924290708990.6182373836541.749673918660.00721195482709-0.0688567498760.1154341292190.05140622727850.0739148535116-0.293061807130.0005219023788530.1010470772210.0423872303640.29294558525-0.0675310182472-0.0271020619890.256869351001-0.01333892986430.31199465031823.229554197165.362582026639.8989104993
102.607121964261.35553467941-0.09759466022635.751572044580.8155702475832.63038176649-0.28581450999-0.5288836474170.4608332543020.4511879395690.33511742661-1.30427563941-0.4380400672160.749129940974-0.2745692059040.456914261918-0.0246177394514-0.1141734809520.707465980681-0.1474119290960.77842772911639.228547649467.638262474542.7490921251
112.697949110970.404196873237-0.2463610770472.489241040560.736934924471.94079373363-0.07002203542540.239479942914-0.0177776360767-0.2169289083030.060387295109-0.158339781467-0.00123160017129-0.03928390638360.0249049266270.3198824524980.03773033503990.05252631128530.2941368173660.005190349436420.27667698557619.092765716126.955933591612.6328235581
124.586256822470.5559159130491.415558250346.330645037614.686499691543.72780506723-0.1125119705780.479443402475-0.0914267985309-0.4236699738280.41490957547-0.7642642381570.06299725121570.548750237094-0.03292000950430.4323187979090.04839943202240.1008563249540.534647963945-0.02299017299160.56252524011134.184251883423.85210305595.66047117119
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 122 )AA1 - 1221 - 122
22chain 'A' and (resid 123 through 200 )AA123 - 200123 - 200
33chain 'A' and (resid 201 through 222 )AA201 - 222201 - 220
44chain 'A' and (resid 223 through 284 )AA223 - 284221 - 282
55chain 'B' and (resid 1 through 122 )BB1 - 1221 - 122
66chain 'B' and (resid 123 through 200 )BB123 - 200123 - 200
77chain 'B' and (resid 201 through 222 )BB201 - 222201 - 222
88chain 'B' and (resid 223 through 284 )BB223 - 284223 - 284
99chain 'B' and (resid 285 through 365 )BB285 - 365285 - 365
1010chain 'B' and (resid 366 through 405 )BB366 - 405366 - 396
1111chain 'A' and (resid 285 through 365 )AA285 - 365283 - 363
1212chain 'A' and (resid 366 through 405 )AA366 - 405364 - 395

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