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- PDB-2yk6: Structure of Neisseria LOS-specific sialyltransferase (NST), in c... -

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Basic information

Entry
Database: PDB / ID: 2yk6
TitleStructure of Neisseria LOS-specific sialyltransferase (NST), in complex with CDP.
ComponentsCMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE
KeywordsTRANSFERASE / LIPOOLIGOSACCHARIDE SIALYLTRANSFERASE
Function / homology
Function and homology information


N-acetyllactosaminide alpha-2,3-sialyltransferase / lipopolysaccharide biosynthetic process / glycosyltransferase activity / 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
CYTIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.83 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 1.2Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.3Sep 4, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)38,3034
Polymers37,5651
Non-polymers7383
Water1,45981
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)76,6058
Polymers75,1302
Non-polymers1,4756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12380 Å2
ΔGint-119.3 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.099, 123.510, 41.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 37565.203 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, EC: 2.4.99.-
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsE40D, R102W, G168I, 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: 2.96 Å3/Da / Density % sol: 58.45 % / 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: 100 MM SODIUM ACETATE (PH 4.2 - 4.4) 1.7 M DI-AMMONIUM SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / 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: 2.83→70.71 Å / Num. obs: 11162 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.4
Reflection shellResolution: 2.83→2.88 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.7 / % possible all: 97.8

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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 2YK5

2yk5


Resolution: 2.83→70.71 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.501 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25654 532 4.8 %RANDOM
Rwork0.18985 ---
obs0.19294 10631 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.83→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 46 81 2764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222751
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9883722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88323.852122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212045
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_it0.7561.51626
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45622638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95331125
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3374.51084
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: 2.827→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 37 -
Rwork0.291 746 -
obs--96.55 %

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