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- PDB-2yk5: Structure of Neisseria LOS-specific sialyltransferase (NST), in c... -

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Basic information

Entry
Database: PDB / ID: 2yk5
TitleStructure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP.
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
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / N-acetyllactosaminide alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 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 1.2Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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)39,1509
Polymers38,0811
Non-polymers1,0698
Water3,963220
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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)78,30018
Polymers76,1622
Non-polymers2,13816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area14290 Å2
ΔGint-145.3 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.747, 124.137, 41.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#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: 38081.039 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

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 56 % / 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: 2.33→70.53 Å / Num. obs: 19839 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 17
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 3.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.32→70.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.898 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22334 1013 5.1 %RANDOM
Rwork0.17645 ---
obs0.17881 18879 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.16 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.32→70.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 65 220 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9913751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.74123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6881514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212054
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_it0.9531.51631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77622646
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.83131145
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4644.51105
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: 2.321→2.381 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 53 -
Rwork0.195 1203 -
obs--86.74 %

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