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- PDB-5wc8: Structure of a bacterial polysialyltransferase at 2.75 Angstrom r... -

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Basic information

Entry
Database: PDB / ID: 5wc8
TitleStructure of a bacterial polysialyltransferase at 2.75 Angstrom resolution
ComponentsSiaD
KeywordsMEMBRANE PROTEIN / polysialyltransferase / GT-B
Function / homologyAlpha-2,8-polysialyltransferase / Alpha-2,8-polysialyltransferase (POLYST) / nucleotide binding / BROMIDE ION / SiaD
Function and homology information
Biological speciesMannheimia haemolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsWorrall, L.J. / Lizak, C. / Strynadka, N.C.J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
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
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: SiaD
A: SiaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,48738
Polymers90,6102
Non-polymers2,87736
Water91951
1
M: SiaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58417
Polymers45,3051
Non-polymers1,27816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SiaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90321
Polymers45,3051
Non-polymers1,59820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.080, 78.080, 303.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SiaD


Mass: 45305.051 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: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.24 %
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: ALS / Beamline: 5.0.2 / Wavelength: 0.91982 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91982 Å / Relative weight: 1
ReflectionResolution: 2.75→61.76 Å / Num. obs: 29021 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 21.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 22.2 % / Rmerge(I) obs: 1.975 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→61.76 Å / SU B: 13.742 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.031 / ESU R Free: 0.327 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1431 4.9 %RANDOM
Rwork0.19 ---
obs0.193 27542 99.9 %-
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.75→61.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 36 51 6456

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