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- PDB-8csc: WbbB D232N-Kdo adduct -

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Basic information

Entry
Database: PDB / ID: 8csc
TitleWbbB D232N-Kdo adduct
ComponentsN-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / Glycsoyltransferase / retaining / donor adduct
Function / homology
Function and homology information


polysaccharide transport / polysaccharide biosynthetic process / transferase activity
Similarity search - Function
: / Glycosyltransferase 99 family N-terminal domain / Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Putative N-acetyl glucosaminyl transferase
Similarity search - Component
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)93,50611
Polymers92,2562
Non-polymers1,2509
Water7,494416
1
A: N-acetyl glucosaminyl transferase
hetero molecules

A: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,47010
Polymers92,2562
Non-polymers1,2158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6140 Å2
ΔGint-61 kcal/mol
Surface area32470 Å2
MethodPISA
2
B: N-acetyl glucosaminyl transferase
hetero molecules

B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,54112
Polymers92,2562
Non-polymers1,28610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6230 Å2
ΔGint-77 kcal/mol
Surface area31990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 158.220, 117.570
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
11A-808-

HOH

21B-808-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 46127.781 Da / Num. of mol.: 2 / Mutation: D232N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wbbB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U8B0
#3: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 423 molecules

#2: 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
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.36 % / Description: prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 100 mM HEPES, 0.5 % Jeffamine ED-2001

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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: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→39.96 Å / Num. obs: 68061 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 36.96 Å2 / Rsym value: 0.038 / Net I/σ(I): 31.8
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5067 / CC1/2: 0.78 / Rsym value: 0.965 / % possible all: 99.9

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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: 1.9→39.96 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 3405 5 %
Rwork0.1871 64656 -
obs0.1887 68061 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 77 416 6735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326571
X-RAY DIFFRACTIONf_angle_d0.53968953
X-RAY DIFFRACTIONf_chiral_restr0.0406992
X-RAY DIFFRACTIONf_plane_restr0.00331159
X-RAY DIFFRACTIONf_dihedral_angle_d13.45182329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.34031420.31152680X-RAY DIFFRACTION99.89
1.93-1.960.32691390.30452657X-RAY DIFFRACTION99.86
1.96-1.990.3181410.28322666X-RAY DIFFRACTION99.79
1.99-2.020.3071400.26172660X-RAY DIFFRACTION99.82
2.02-2.050.2511410.24382672X-RAY DIFFRACTION99.82
2.05-2.090.28681400.23072664X-RAY DIFFRACTION99.96
2.09-2.130.26821420.22872691X-RAY DIFFRACTION99.86
2.13-2.170.2461400.22612651X-RAY DIFFRACTION99.86
2.17-2.220.2471410.22122685X-RAY DIFFRACTION99.79
2.22-2.270.30561400.22982648X-RAY DIFFRACTION99.79
2.27-2.330.27041410.22652673X-RAY DIFFRACTION99.72
2.33-2.390.24861410.21562678X-RAY DIFFRACTION99.86
2.39-2.460.26321410.21612681X-RAY DIFFRACTION99.86
2.46-2.540.24551420.21182693X-RAY DIFFRACTION99.96
2.54-2.630.28911410.21522681X-RAY DIFFRACTION99.96
2.63-2.740.25141410.21092690X-RAY DIFFRACTION100
2.74-2.860.29431430.2242706X-RAY DIFFRACTION99.96
2.86-3.020.28441410.21322684X-RAY DIFFRACTION99.93
3.02-3.20.22991420.20382704X-RAY DIFFRACTION99.93
3.2-3.450.18411430.17592710X-RAY DIFFRACTION100
3.45-3.80.1951430.16122725X-RAY DIFFRACTION99.93
3.8-4.350.16161440.14042734X-RAY DIFFRACTION99.83
4.35-5.480.15541460.14282762X-RAY DIFFRACTION99.97
5.48-39.960.20471500.172861X-RAY DIFFRACTION99.57
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)
11.08583987425-0.339631927127-0.1614468140353.06350579569-1.037323634151.981086646680.03581583428850.314866789194-0.0111564050293-0.8839656466390.07422383855790.2531965886340.498412680958-0.307013579693-0.09079296577750.475316138435-0.0851969014505-0.01807061380950.4049974872670.04091587640920.33676855168921.59760875730.1568947931-34.7606803108
22.179054773461.63044270416-0.2290498555642.1146810797-1.270865664022.42861418609-0.0822776639896-0.193228209786-0.1820741941960.8093597433760.08355727776930.1629723596610.0881129622677-0.230571428977-0.007964262479760.404463341188-0.02282510814710.03559601113310.373703689870.03938327316550.26785220861525.599889368724.1821675431-5.16273066107
32.8334286930.696822471519-1.098428447492.18394616215-0.05087246299782.82655739734-0.0592827271787-0.0757213864032-0.213045629845-0.0584374699585-0.00161500193018-0.4401807752830.2046442429620.3397048173180.04391372194530.28453481977-0.01184125941450.07188814662460.3405091518960.02562781135670.38962507641342.105958450521.3865251272-17.2024375614
42.512883755540.175077896907-0.04785530045463.44647994337-1.601766257853.315786147480.0674550686435-0.1197790178180.1737526064370.3156746181720.3099454861210.650936013969-0.154755463514-0.619173677767-0.3092019670890.248725551881-0.032675177870.09649077242120.3877708407520.07786217934330.39175100617616.233969163327.8976500128-9.78142537033
53.593574059540.46487355394-0.4172466591612.92639901513-0.5932070496241.899687532880.166714239408-0.7079749449340.3942286619171.67192433991-0.002969908452360.139403689008-1.35375079659-0.118681685593-0.2095426574681.155752676890.08307071088240.1734902903650.504703606502-0.001260836102850.41659402740824.117975119967.8232573304-12.8489777861
60.9179086211850.549010772237-0.2835670981574.73811881586-2.160037940222.727588323550.0413044536641-0.105691524373-0.02033818606610.4631499359750.1593547139810.359304964887-0.217518840154-0.217658794831-0.2081904940470.2258217117250.05834140942820.04484904286550.260940519490.01990186451130.26597928849823.009965992956.5641931655-25.5297032943
74.08955455-1.547289034840.9836538035613.75873848909-0.9888666511292.53970043673-0.0006357911014470.2027709450820.2770804308660.0676354421056-0.0458313043406-0.340113044866-0.2282423213360.2122547833690.01990655897770.2399310612540.00843373332857-0.02276850829730.237182398334-0.009158173575870.22187458408136.003842116972.9361687566-40.9204703873
81.65265968452-0.4128778219160.1347751243462.90788791721-0.7217718748162.48827281307-0.05078698249240.0793529435283-0.0627533109198-0.04754092097190.5138355818941.25457677005-0.175359815759-0.854799649268-0.2410366958520.2781283615830.122640093824-0.01530764679520.5309411854650.1997441813870.67684077064712.177067547263.980882634-38.2614676219
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 183 )AA1 - 1831 - 183
22chain 'A' and (resid 184 through 222 )AA184 - 222184 - 220
33chain 'A' and (resid 223 through 321 )AA223 - 321221 - 319
44chain 'A' and (resid 322 through 405 )AA322 - 405320 - 394
55chain 'B' and (resid 1 through 94 )BB1 - 941 - 94
66chain 'B' and (resid 95 through 200 )BB95 - 20095 - 200
77chain 'B' and (resid 201 through 321 )BB201 - 321201 - 321
88chain 'B' and (resid 322 through 403 )BB322 - 403322 - 393

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