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- PDB-8csb: WbbB D232N in complex with CMP-beta-Kdo -

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Basic information

Entry
Database: PDB / ID: 8csb
TitleWbbB D232N in complex with CMP-beta-Kdo
ComponentsN-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / Glycsoyltransferase / retaining / donor complex
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / CYTIDINE-5'-MONOPHOSPHATE / Chem-CMK / PHOSPHATE ION / Putative N-acetyl glucosaminyl transferase
Function and homology information
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

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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)94,33710
Polymers92,2242
Non-polymers2,1138
Water1,53185
1
A: N-acetyl glucosaminyl transferase
hetero molecules

A: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,52712
Polymers92,2242
Non-polymers2,30310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7650 Å2
ΔGint-50 kcal/mol
Surface area32080 Å2
MethodPISA
2
B: N-acetyl glucosaminyl transferase
hetero molecules

B: N-acetyl glucosaminyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1478
Polymers92,2242
Non-polymers1,9236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7010 Å2
ΔGint-32 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.710, 157.440, 120.060
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

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Components

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


Mass: 46111.781 Da / Num. of mol.: 2 / Mutation: D232N
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: 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-CMK / CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID / CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID


Mass: 543.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N3O15P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.43 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM NaCl, 100 mM HEPES, 1.6 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→48 Å / Num. obs: 41916 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 59.82 Å2 / Rsym value: 0.071 / Net I/σ(I): 11.71
Reflection shellResolution: 2.25→2.31 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 3016 / Rsym value: 0.8

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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: 2.25→47.99 Å / SU ML: 0.3629 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.9051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 2094 5 %
Rwork0.2029 39795 -
obs0.205 41889 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.14 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 134 85 6446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01456518
X-RAY DIFFRACTIONf_angle_d1.36878878
X-RAY DIFFRACTIONf_chiral_restr0.0685988
X-RAY DIFFRACTIONf_plane_restr0.01051131
X-RAY DIFFRACTIONf_dihedral_angle_d16.02212280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.40411360.35352588X-RAY DIFFRACTION99.63
2.3-2.360.33051390.29652626X-RAY DIFFRACTION99.64
2.36-2.420.34741370.26392608X-RAY DIFFRACTION99.75
2.42-2.50.28671390.2642636X-RAY DIFFRACTION99.82
2.5-2.580.28231370.25842630X-RAY DIFFRACTION99.78
2.58-2.670.31351390.26372632X-RAY DIFFRACTION99.86
2.67-2.770.30711390.28532633X-RAY DIFFRACTION99.93
2.77-2.90.36281390.28952643X-RAY DIFFRACTION99.82
2.9-3.050.30291390.25152636X-RAY DIFFRACTION99.86
3.05-3.240.30881390.25182640X-RAY DIFFRACTION99.82
3.24-3.50.29011400.23922662X-RAY DIFFRACTION99.89
3.5-3.850.26091390.19142666X-RAY DIFFRACTION99.79
3.85-4.40.2081410.16512677X-RAY DIFFRACTION99.75
4.4-5.550.19821420.15732707X-RAY DIFFRACTION99.89
5.55-47.990.18771490.16712811X-RAY DIFFRACTION99.6
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)
11.19591287390.313151428632-0.06115276737394.734863963131.841971651363.572744386370.142175956285-0.231358404139-0.0264476314770.9249687881850.0766986017559-0.4025640114790.6319434643250.376071131813-0.1953774506020.5191680162380.09032110553780.006812188892130.5200146675890.001317526213450.55361153438324.751303548529.449126964231.2626001817
28.09069808928-1.54854190895-1.287478464632.77697401582-1.303421840892.78537189783-0.05054750884470.470049130595-0.78053442445-0.236954022911-0.1189444172980.200381689160.3069203717350.126741085780.2310408676940.5019920451230.02990521012260.154482697880.407796064139-0.04104587230790.5501295433038.5537429295320.36591293317.9676640303
36.06108209123-1.65142484778-0.4116190883066.31129341581.339555601394.085163072030.04437639760130.0518156294893-0.5038375800670.0856811173529-0.2292709085141.012605111940.246462636124-0.500483384060.1140446230580.4233195044140.01746811101690.09069647530450.437283604848-0.04593060317740.5396561104873.314780190418.801349690616.2370602452
43.07889210291-0.09582771702431.397638313434.664681054861.982525384955.297639086420.06321380630720.2355862629540.213132334808-0.5734595714820.427831418556-0.920753576795-0.09744908804340.912999937504-0.4497010846290.4922475014110.06133903197950.219848238230.586937106854-0.07861548036590.66939815521129.742822417527.896891405710.1596162684
53.597968784222.57533450378-1.917297285524.940179758430.7412798180612.85422911940.2317889972890.3782760986870.32476342847-1.570243860040.183541891703-0.521506675975-1.819856043680.528049133209-0.3696434935171.52994130294-0.2332890812780.3149489156780.674200207299-0.004536664079420.62182012867424.649116165764.880278689716.085308285
63.671428756023.00504778393-1.132793914487.25130522881-0.3243891282921.9034348971-0.02238149835810.4629162404061.11275457827-2.356948551230.04336175758660.929249225812-1.65033359080.02911431908440.1384136453662.10119252837-0.1514490336530.1550101661880.7124935150220.05449590758161.1038114086620.985718131176.153902417113.5192380265
71.88677522312-1.84056075643-2.212449207065.73942376702-0.6246263499875.312552619210.6174666806180.0849252663003-0.166537945487-1.81934706-0.555903068210.0599339496427-1.728594763590.159969780793-0.02192317494971.301201243110.000641843348394-0.01494456278650.643363576619-0.07122264416380.43443792670516.594907911961.07535660213.4013409339
80.957491923342-0.006726771833720.3136088880357.126297937922.363564433382.809182472470.0571564142388-0.02023785492970.102134518212-0.696677241030.345768918991-0.886252873145-0.378949643440.493361311298-0.4724667972270.392685290941-0.1037247757750.1498071102130.520144133997-0.04861478519340.56264240164326.389865961457.241862217628.5650414561
97.916538725434.865696570784.856634412754.60054532774.351389325695.9892378688-0.00369817260517-0.1746936379730.706553160523-0.256149489501-0.4509673516310.443053871823-0.297278844631-0.1876041473630.4174881646950.5091995567660.003417119146040.0295509127660.3309107483580.05606443351560.60068435291111.940293005770.897635479539.1221206351
105.467679478241.89360307922-0.04011398641369.038885354940.3529834920339.25043640034-0.0431432689578-0.1358314582980.778872740973-0.110616597467-0.3095248724451.15890729329-0.731450216579-0.9346518922110.1902812786670.4759139793160.105295720628-0.06493217869170.459461439183-0.064623994150.6889288632222.2655141472575.126894458640.2997414332
113.370890990010.501505791998-0.4272043271645.256397584381.494041018293.102873365480.006489923666830.04045243160660.0574496764876-0.246055761720.329729960121-1.03175687077-0.1270708423530.507045220823-0.349938623390.39917109623-0.137716664040.009557248505790.45666525972-0.04026042492320.53223005319323.560224383564.923801911440.5332673716
122.971102937521.044821918241.481498539866.023275349880.9586831067343.67687560399-0.260149652112-0.8350935499610.2734101617090.1012180089220.614340183548-2.66717963062-0.2432626346430.963613245316-0.2122714762110.531513707373-0.146652231848-0.1138605569961.27646649571-0.3737534966561.4350444677240.156996615665.053792254442.0719864109
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 208 )AA1 - 2081 - 208
22chain 'A' and (resid 209 through 243 )AA209 - 243209 - 243
33chain 'A' and (resid 244 through 321 )AA244 - 321244 - 321
44chain 'A' and (resid 322 through 404 )AA322 - 404322 - 394
55chain 'B' and (resid 1 through 38 )BB1 - 381 - 38
66chain 'B' and (resid 39 through 64 )BB39 - 6439 - 64
77chain 'B' and (resid 65 through 107 )BB65 - 10765 - 107
88chain 'B' and (resid 108 through 208 )BB108 - 208108 - 208
99chain 'B' and (resid 209 through 243 )BB209 - 243209 - 243
1010chain 'B' and (resid 244 through 284 )BB244 - 284244 - 284
1111chain 'B' and (resid 285 through 365 )BB285 - 365285 - 365
1212chain 'B' and (resid 366 through 401 )BB366 - 401366 - 391

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