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- PDB-2yk4: Structure of Neisseria LOS-specific sialyltransferase (NST). -

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Basic information

Entry
Database: PDB / ID: 2yk4
TitleStructure of Neisseria LOS-specific sialyltransferase (NST).
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
N-acetyllactosaminide alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 1.2Sep 25, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,0956
Polymers38,2101
Non-polymers8855
Water4,558253
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)78,19012
Polymers76,4202
Non-polymers1,77010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area13490 Å2
ΔGint-92.3 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.565, 124.735, 41.866
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: 38210.152 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-EGC / 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL / TRITON X-100


Mass: 602.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58O10 / Comment: detergent*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsE40D, R102W, G168I, T242A, AND K273N ARE NATURAL VARIANTS IN THE STRAIN N. MENINGITIDIS SEROTYPE B ...E40D, R102W, G168I, T242A, 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: 2.97 Å3/Da / Density % sol: 58.65 % / 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→71.07 Å / Num. obs: 34365 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 35.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.22 / % possible all: 99.9

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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 2YK5

2yk5


Resolution: 1.94→71.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.108 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22274 1735 5.1 %RANDOM
Rwork0.19499 ---
obs0.19639 32604 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.485 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2--0.23 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.94→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 59 253 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222766
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9913732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98723.852122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9391513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212052
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_it1.0361.51631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8222646
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57631135
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9534.51086
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: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 115 -
Rwork0.246 2399 -
obs--99.13 %

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