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- PDB-5n80: glycosyltransferase LPS biosynthesis in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 5n80
Titleglycosyltransferase LPS biosynthesis in complex with UDP
ComponentsLipopolysaccharide 1,6-galactosyltransferase
KeywordsTRANSFERASE / LPS biosynthesis Glycosyltranferase UDP
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / lipopolysaccharide core region biosynthetic process / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / URIDINE-5'-DIPHOSPHATE / Lipopolysaccharide 1,6-galactosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.92 Å
AuthorsZhang, Z. / Ashworth, G.J.
CitationJournal: To Be Published
Title: glycosyltransferase LPS biosynthesis in complex with UDP
Authors: Zhang, Z. / Ashworth, G.J.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 2.0Apr 25, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / refine / refine_hist / software / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_seq_id / _entity.pdbx_description / _entity.type / _pdbx_struct_special_symmetry.auth_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid
Revision 3.0Jun 12, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _atom_site.occupancy / _audit_author.name / _citation_author.name
Revision 3.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide 1,6-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4182
Polymers41,0141
Non-polymers4041
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-3 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.440, 104.440, 89.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-533-

HOH

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Components

#1: Protein Lipopolysaccharide 1,6-galactosyltransferase / UDP-D-galactose--(Glucosyl)lipopolysaccharide-alpha-1 / 3-D-galactosyltransferase


Mass: 41014.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UDP
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: rfaB, waaB, STM3719 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q06994, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 1% trypton; 0.001M sodium azide; 0.05M HEPES pH7.0 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→73.85 Å / Num. obs: 38460 / % possible obs: 99.5 % / Redundancy: 16 % / Net I/σ(I): 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data collection
xia2data scaling
RefinementResolution: 1.92→73.85 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.271 1978 5.15 %
Rwork0.239 --
obs0.241 38396 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→73.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 25 81 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082950
X-RAY DIFFRACTIONf_angle_d0.9153994
X-RAY DIFFRACTIONf_dihedral_angle_d14.2971741
X-RAY DIFFRACTIONf_chiral_restr0.057430
X-RAY DIFFRACTIONf_plane_restr0.007502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9680.32221480.31212535X-RAY DIFFRACTION99
1.968-2.02120.31711310.30242546X-RAY DIFFRACTION100
2.0212-2.08070.29881100.29012600X-RAY DIFFRACTION100
2.0807-2.14790.30261560.2652532X-RAY DIFFRACTION100
2.1479-2.22460.32321300.2592582X-RAY DIFFRACTION100
2.2246-2.31370.29471560.25362558X-RAY DIFFRACTION100
2.3137-2.4190.31341390.25592582X-RAY DIFFRACTION100
2.419-2.54660.32851310.27132599X-RAY DIFFRACTION100
2.5466-2.70610.31951290.28982589X-RAY DIFFRACTION100
2.7061-2.91510.33571440.28772598X-RAY DIFFRACTION100
2.9151-3.20840.34061500.28132606X-RAY DIFFRACTION100
3.2084-3.67270.27361310.23212633X-RAY DIFFRACTION100
3.6727-4.62710.21211520.17992668X-RAY DIFFRACTION100
4.6271-73.90490.20111710.18782790X-RAY DIFFRACTION100

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