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- PDB-8sv2: Pasteurella multocida alpha2,3/2,6 sialyltransferase D141N bound ... -

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Basic information

Entry
Database: PDB / ID: 8sv2
TitlePasteurella multocida alpha2,3/2,6 sialyltransferase D141N bound to CMP
ComponentsAlpha-2,3/2,6-sialyltransferase/sialidase
KeywordsSUGAR BINDING PROTEIN / sialyltransferase / CMP
Function / homologySialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / glycosyltransferase activity / CYTIDINE-5'-MONOPHOSPHATE / TRIETHYLENE GLYCOL / Alpha-2,3/2,6-sialyltransferase/sialidase
Function and homology information
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsStubbs, H.E. / Iverson, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Veterans Affairs (VA, United States)R01AI130684 United States
Department of Veterans Affairs (VA, United States)R01AI106987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137458 United States
American Heart Association14GRNT20390021 United States
CitationJournal: To Be Published
Title: Pasteurella multocida alpha2,3/2,6 sialyltransferase D141N bound to CMP
Authors: Stubbs, H.E. / Iverson, T.M.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9705
Polymers45,2241
Non-polymers7464
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.598, 66.401, 96.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha-2,3/2,6-sialyltransferase/sialidase


Mass: 45224.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15KI8
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 14 mg/mL PMSTD141N protein in 20 mM Tris pH 7.5 mother liquor: 23% PEG 3350 100 mM HEPES, pH 6.0 100 mM NaCl 0.4% Triton X-100 5 mM CMP Drops were 1:1 protein and mother liquor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12704 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12704 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 38024 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 47.83
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 1849 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→31.89 Å / SU ML: 0.2124 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 1867 4.92 %
Rwork0.215 36076 -
obs0.2169 37943 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 46 224 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823254
X-RAY DIFFRACTIONf_angle_d1.02334417
X-RAY DIFFRACTIONf_chiral_restr0.0559487
X-RAY DIFFRACTIONf_plane_restr0.0062567
X-RAY DIFFRACTIONf_dihedral_angle_d7.0251433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.31051510.27692557X-RAY DIFFRACTION93.7
1.89-1.950.26221550.25332721X-RAY DIFFRACTION99.72
1.95-2.010.2721340.25132765X-RAY DIFFRACTION99.93
2.01-2.080.29571570.2592722X-RAY DIFFRACTION99.79
2.08-2.170.35621570.24972742X-RAY DIFFRACTION99.93
2.17-2.270.28471570.23772756X-RAY DIFFRACTION100
2.27-2.380.27681170.23432789X-RAY DIFFRACTION99.9
2.38-2.530.31061350.23152772X-RAY DIFFRACTION99.93
2.53-2.730.28271300.22892811X-RAY DIFFRACTION99.93
2.73-30.28621320.23692814X-RAY DIFFRACTION99.93
3-3.440.27011380.21622804X-RAY DIFFRACTION99.9
3.44-4.330.19521620.18032837X-RAY DIFFRACTION100
4.33-31.890.21471420.18712986X-RAY DIFFRACTION99.84

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