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- PDB-5fa0: The structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid tra... -

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Basic information

Entry
Database: PDB / ID: 5fa0
TitleThe structure of the beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase domain from WbbB
ComponentsPutative N-acetyl glucosaminyl transferase
KeywordsTRANSFERASE / LPS biosynthesis / glycosyltransferase
Function / homology: / Glycosyltransferase 99 family N-terminal domain / Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / Putative N-acetyl glucosaminyl transferase
Function and homology information
Biological speciesRaoultella terrigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)92,8863
Polymers92,8502
Non-polymers351
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-28 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 82.930, 120.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative N-acetyl glucosaminyl transferase


Mass: 46425.031 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): B834(DE3) / References: UniProt: Q6U8B0
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 mg/ml WbbB, 0.2M MgCl2, 0.1 M Tris.HCl, 25 % PEG 4000, 10 mM tris(2-carboxyethyl)phosphine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97836 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 7, 2015
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97836 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 71295 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 20.44 Å2 / Rsym value: 0.073 / Net I/σ(I): 19.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.465 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1141 3.03 %
Rwork0.1855 --
obs0.1868 37670 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 1 562 6779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036397
X-RAY DIFFRACTIONf_angle_d0.6368697
X-RAY DIFFRACTIONf_dihedral_angle_d12.1162291
X-RAY DIFFRACTIONf_chiral_restr0.026965
X-RAY DIFFRACTIONf_plane_restr0.0021128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.25461410.22424497X-RAY DIFFRACTION100
2.4047-2.53140.25681410.21534481X-RAY DIFFRACTION100
2.5314-2.690.27641410.21164522X-RAY DIFFRACTION100
2.69-2.89770.19731400.20634507X-RAY DIFFRACTION100
2.8977-3.18920.30431430.20194558X-RAY DIFFRACTION100
3.1892-3.65040.22011400.18444564X-RAY DIFFRACTION100
3.6504-4.59820.21571420.14984612X-RAY DIFFRACTION100
4.5982-41.47170.18411530.16574788X-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)
13.73990.24290.07181.32690.18082.34380.00140.10930.193-0.0272-0.0266-0.1129-0.0536-0.01130.00970.1110.02970.0345-0.0187-0.01870.163926.1413-40.491138.8671
21.25180.34580.64320.987-0.42961.4674-0.5018-0.71220.5949-0.05180.1680.3775-0.7119-0.72380.07360.15320.2981-0.04890.6122-0.21390.3217-0.8032-30.22550.1315
32.9136-0.62130.09182.02830.57623.9608-0.2417-0.82150.05930.39910.1336-0.1735-0.0957-0.326-0.00040.20630.0822-0.0290.4695-0.07280.017418.395-39.004665.3367
43.8102-0.1801-0.51551.71660.07021.6756-0.02350.1176-0.2320.0854-0.00060.06890.24950.107-0.00150.1483-0.01620.00080.0384-0.01280.1467-27.145-40.087834.1901
52.9454-0.92981.03362.6950.19213.6138-0.18480.42890.5567-0.0991-0.009-0.4677-0.4830.29090.14560.18490.0062-0.0040.4014-0.01070.224-0.2384-28.410623.6014
62.2164-0.0568-0.06422.06560.46443.1565-0.10311.64530.0961-0.620.2589-0.0875-0.0134-0.12540.03360.3125-0.04880.00750.9315-0.0983-0.0441-18.8208-35.70389.0245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:156 )A1 - 156
2X-RAY DIFFRACTION2( CHAIN A AND RESID 222:320 )A222 - 320
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 157:212 OR RESID 321:407 ) )A157 - 212
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 157:212 OR RESID 321:407 ) )A321 - 407
5X-RAY DIFFRACTION4( CHAIN B AND RESID 1:156 )B1 - 156
6X-RAY DIFFRACTION5( CHAIN B AND RESID 222:320 )B222 - 320
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 157:216 OR RESID 321:402 ) )B157 - 216
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 157:216 OR RESID 321:402 ) )B321 - 402

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