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- PDB-5wd7: Structure of a bacterial polysialyltransferase in complex with fo... -

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Basic information

Entry
Database: PDB / ID: 5wd7
TitleStructure of a bacterial polysialyltransferase in complex with fondaparinux
ComponentsSiaD
KeywordsMEMBRANE PROTEIN / polysialyltransferase / GT-B
Function / homologyAlpha-2,8-polysialyltransferase / Alpha-2,8-polysialyltransferase (POLYST) / nucleotide binding / fondaparinux / SiaD
Function and homology information
Biological speciesMannheimia haemolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWorrall, L.J. / Lizak, C. / Strynadka, N.C.J.
CitationJournal: Sci Rep / Year: 2017
Title: X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid.
Authors: Lizak, C. / Worrall, L.J. / Baumann, L. / Pfleiderer, M.M. / Volkers, G. / Sun, T. / Sim, L. / Wakarchuk, W. / Withers, S.G. / Strynadka, N.C.J.
History
DepositionJul 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _refine_hist.d_res_low
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SiaD
M: SiaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4315
Polymers90,7302
Non-polymers1,7003
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-40 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.312, 78.312, 299.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21M

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 20 - 401 / Label seq-ID: 1 - 382

Dom-IDAuth asym-IDLabel asym-ID
1AA
2MB

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Components

#1: Protein SiaD


Mass: 45365.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia haemolytica (bacteria) / Gene: siaD / Production host: Escherichia coli (E. coli) / References: UniProt: G4RIN4
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside / fondaparinux


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1508.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: fondaparinux
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 17% - 24% PEG3350 (v/v), 140 - 250 mM Mg2SO4 and 100 mM MES pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.00635 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00635 Å / Relative weight: 1
ReflectionResolution: 3.1→44.93 Å / Num. obs: 20333 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.054 / Rrim(I) all: 0.148 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.317.41.3920.5860.5451.497100
8.77-44.936.10.02210.0090.02499.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→44.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.514 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 938 4.6 %RANDOM
Rwork0.18725 ---
obs0.1896 19333 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.079 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.42 Å20 Å2
2---0.83 Å20 Å2
3---2.7 Å2
Refinement stepCycle: 1 / Resolution: 3.1→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 101 0 6481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196649
X-RAY DIFFRACTIONr_bond_other_d0.0020.026418
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9878939
X-RAY DIFFRACTIONr_angle_other_deg0.965314971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69124.061293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.645151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4641533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021335
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_it6.0028.5213069
X-RAY DIFFRACTIONr_mcbond_other6.0028.5213068
X-RAY DIFFRACTIONr_mcangle_it9.312.793838
X-RAY DIFFRACTIONr_mcangle_other9.29912.7893839
X-RAY DIFFRACTIONr_scbond_it6.3449.2283580
X-RAY DIFFRACTIONr_scbond_other6.3439.2283581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.99813.5595102
X-RAY DIFFRACTIONr_long_range_B_refined15.06526780
X-RAY DIFFRACTIONr_long_range_B_other15.06526781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23666 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2M
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 66 -
Rwork0.338 1376 -
obs--99.86 %

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