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- PDB-2yk7: Structure of Neisseria LOS-specific sialyltransferase (NST), in c... -

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Basic information

Entry
Database: PDB / ID: 2yk7
TitleStructure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP-3F-Neu5Ac.
ComponentsCMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


N-acetyllactosaminide alpha-2,3-sialyltransferase / N-acetyllactosaminide alpha-2,3-sialyltransferase activity / lipopolysaccharide biosynthetic process / cell outer membrane
Similarity search - Function
Barnase; Chain D - #20 / Glycosyltransferase family 52 / Glycosyltransferase family 52 / Barnase; Chain D / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CSF / N-acetyllactosaminide alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLin, L.Y.C. / Rakic, B. / Chiu, C.P.C. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Mechanism of the Lipooligosaccharide Sialyltransferase from Neisseria Meningitidis
Authors: Lin, L.Y.C. / Rakic, B. / Chiu, C.P.C. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
History
DepositionMay 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Dec 3, 2014Group: Data collection
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4554
Polymers37,5221
Non-polymers9333
Water2,666148
1
A: CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
hetero molecules

A: CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9108
Polymers75,0442
Non-polymers1,8666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12830 Å2
ΔGint-86 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.762, 101.413, 166.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE / ALPHA 2\ / 3-ST / BETA-GALACTOSIDE ALPHA-2\ / 3-SIALYL TRANSFERASE / LIPOOLIGOSACCHARIDE ...ALPHA 2\ / 3-ST / BETA-GALACTOSIDE ALPHA-2\ / 3-SIALYL TRANSFERASE / LIPOOLIGOSACCHARIDE SIALYLTRANSFERASE / LOS-SPECIFIC SIALYLTRANSFERASE


Mass: 37522.109 Da / Num. of mol.: 1 / Fragment: DELTA29NST, RESIDUES 49-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
Strain: 126E / NRCC4010 / Variant: L1 IMMUNOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P72097, Transferases; Glycosyltransferases; Transferring other glycosyl groups
#2: Chemical ChemComp-CSF / CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID / CMP-3FNEUAC


Type: RNA linking / Mass: 632.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30FN4O16P
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsE40D, R102W, G168I, T242, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITIDIS SEROTYPE B ...E40D, R102W, G168I, T242, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITIDIS SEROTYPE B 126E / NRCC4010.

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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: 2.44 Å3/Da / Density % sol: 49.52 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 4.4
Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION METHODS USING DROPS OF PROTEIN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT: 180MM TRI-SODIUM CITRATE, 5 MM MNCL2, 20%(V/V) PEG 1500, PH 6.25 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: X-RAY MIRRORS OSMIC VARIMAXHR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.18→83.33 Å / Num. obs: 19377 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 23.9
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.64 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YK4

2yk4


Resolution: 2.18→83.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.671 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25786 957 5.1 %RANDOM
Rwork0.19806 ---
obs0.20103 17844 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.876 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.18→83.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 62 148 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222742
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9913709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08424.016122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66515471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3241512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212037
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9081.51610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56322610
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42531132
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.44.51099
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.181→2.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 66 -
Rwork0.263 1142 -
obs--85.49 %

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