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- PDB-5fa1: The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid tra... -

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Basic information

Entry
Database: PDB / ID: 5fa1
TitleThe structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain of WbbB
ComponentsPutative N-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / LPS biosynthesis / glycosyltransferase
Function / homologyCapsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / CYTIDINE-5'-MONOPHOSPHATE / Putative N-acetyl glucosaminyl transferase
Function and homology information
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMallette, E. / Ovchinnikova, O.G. / Whitfield, C. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
GlycoNETAM-4 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Bacterial beta-Kdo glycosyltransferases represent a new glycosyltransferase family (GT99).
Authors: Ovchinnikova, O.G. / Mallette, E. / Koizumi, A. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,8404
Polymers92,1942
Non-polymers6462
Water15,079837
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-2 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.750, 159.390, 120.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1023-

HOH

21B-1033-

HOH

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Components

#1: Protein Putative N-acetyl glucosaminyl transferase


Mass: 46096.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wbbB / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6U8B0
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10 mg/ml WbbB, 0.2 M NaCl, 0.1M Bis-Tris, 25% PEG 3350, 1 mM TCEP, 1mM CMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2015
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 52154 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.094 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FA0

5fa0


Resolution: 2.1→48.046 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 2608 5 %random selection
Rwork0.1711 ---
obs0.173 52148 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6187 0 42 837 7066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056422
X-RAY DIFFRACTIONf_angle_d0.8278737
X-RAY DIFFRACTIONf_dihedral_angle_d12.842293
X-RAY DIFFRACTIONf_chiral_restr0.033969
X-RAY DIFFRACTIONf_plane_restr0.0041129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.24121350.19992571X-RAY DIFFRACTION100
2.1382-2.17930.23791350.19752558X-RAY DIFFRACTION100
2.1793-2.22380.2161370.19762594X-RAY DIFFRACTION100
2.2238-2.27210.26671350.21512562X-RAY DIFFRACTION100
2.2721-2.3250.23721360.19242594X-RAY DIFFRACTION100
2.325-2.38310.2321360.1782577X-RAY DIFFRACTION100
2.3831-2.44760.2081360.18012596X-RAY DIFFRACTION100
2.4476-2.51960.22431360.17642577X-RAY DIFFRACTION100
2.5196-2.60090.24461360.17622592X-RAY DIFFRACTION100
2.6009-2.69390.25571360.18252587X-RAY DIFFRACTION100
2.6939-2.80170.24681380.18242611X-RAY DIFFRACTION100
2.8017-2.92920.20871360.18232579X-RAY DIFFRACTION100
2.9292-3.08360.2181380.17482622X-RAY DIFFRACTION100
3.0836-3.27680.20321360.17092598X-RAY DIFFRACTION100
3.2768-3.52970.18441380.16052619X-RAY DIFFRACTION100
3.5297-3.88480.21411390.15792634X-RAY DIFFRACTION100
3.8848-4.44660.16621390.1372638X-RAY DIFFRACTION100
4.4466-5.60080.16781390.14262652X-RAY DIFFRACTION100
5.6008-48.05840.18991470.16872779X-RAY DIFFRACTION100
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)
10.88620.14240.18772.41160.56431.87830.0949-0.2103-0.05710.8952-0.0228-0.22960.62450.1169-0.00920.33410.0392-0.05240.1369-0.00550.110325.15630.345237.6455
21.18240.15720.0592.02520.56641.76030.07270.29550.0679-0.9187-0.0465-0.0664-0.6328-0.0214-0.01890.38850.00430.05860.145-0.00060.075421.774261.696815.3738
30.6120.02880.17342.72681.12971.72920.006-0.02710.03060.1735-0.0303-0.02950.2361-0.01120.02660.07420.02450.02790.0961-0.01560.087122.718626.042319.7733
40.76190.1334-0.08142.81470.460.61650.05550.03170.0408-0.3120.0947-0.0748-0.25340.0059-0.0840.1291-0.03990.04250.0585-0.00250.10324.622265.952433.1844
51.32420.00480.10432.08720.52651.392-0.070.06590.0058-0.37890.2083-0.31810.03490.2824-0.02110.12510.04610.05460.1507-0.06970.13429.041226.94829.2813
60.8145-0.2793-0.3741.9680.16730.72570.042-0.26860.15850.36670.407-1.0213-0.24410.33330.10310.007-0.1183-0.11360.1647-0.12490.238133.431264.599541.2846
71.9046-0.3428-0.59791.3791-0.15581.6266-0.08460.072-0.2473-0.1294-0.07810.54390.1808-0.2480.04380.0911-0.01290.03250.1449-0.070.26924.682321.058117.0113
82.14060.42390.27111.974-0.11451.96450.0489-0.10020.20660.0831-0.05380.284-0.1689-0.2665-0.00680.08610.00910.01520.133-0.02560.09338.302371.426241.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:156 )A2 - 156
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:156 )B2 - 156
3X-RAY DIFFRACTION3( CHAIN A AND RESID 157:183 )A157 - 183
4X-RAY DIFFRACTION4( CHAIN B AND RESID 157:183 )B157 - 183
5X-RAY DIFFRACTION5( CHAIN A AND ( RESID 184:215 OR RESID 330:403 ) )A184 - 215
6X-RAY DIFFRACTION5( CHAIN A AND ( RESID 184:215 OR RESID 330:403 ) )A330 - 403
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 184:215 OR RESID 330:401 ) )B184 - 215
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 184:215 OR RESID 330:401 ) )B330 - 401
9X-RAY DIFFRACTION7( CHAIN A AND RESID 220:329 )A220 - 329
10X-RAY DIFFRACTION8( CHAIN B AND RESID 216:329 )B216 - 329

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