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- PDB-8u9i: Pasteurella multocida alpha2,3/2,6 sialyltransferase D141N bound ... -

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Basic information

Entry
Database: PDB / ID: 8u9i
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 / DI(HYDROXYETHYL)ETHER / Alpha-2,3/2,6-sialyltransferase/sialidase
Function and homology information
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionSep 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,4527
Polymers92,9332
Non-polymers5195
Water16,934940
1
A: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7874
Polymers46,4661
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6653
Polymers46,4661
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.916, 60.947, 96.168
Angle α, β, γ (deg.)90.000, 101.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 46466.480 Da / Num. of mol.: 2 / Mutation: D141N
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-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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Hanging drop; PMSTD141N (10mg/mL) in 20 mM Tris pH 7.5 was combined with reservoir buffer (100mM HEPES pH 7.5, 100mM NaCl, 23% PEG3350, 0.4% TritonX-100) at a 1:1 ratio to form 3 uL drops.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 90863 / % possible obs: 86.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 1 / Net I/σ(I): 17.63
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 4510 / CC1/2: 0.702

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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: 1.55→28.99 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.2879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 4544 5.03 %
Rwork0.1791 85839 -
obs0.1808 90383 85.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.07 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 34 940 7326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916550
X-RAY DIFFRACTIONf_angle_d0.97988882
X-RAY DIFFRACTIONf_chiral_restr0.059971
X-RAY DIFFRACTIONf_plane_restr0.00741147
X-RAY DIFFRACTIONf_dihedral_angle_d15.96852403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.560.28311510.21372529X-RAY DIFFRACTION76.68
1.56-1.580.27011240.22082915X-RAY DIFFRACTION86.41
1.58-1.60.29141310.21262863X-RAY DIFFRACTION84.67
1.6-1.620.27051520.21052843X-RAY DIFFRACTION87.04
1.62-1.640.23211380.20942870X-RAY DIFFRACTION84.59
1.64-1.670.26451380.20682915X-RAY DIFFRACTION87.35
1.67-1.690.24411540.20442909X-RAY DIFFRACTION87.12
1.69-1.710.24131550.20552881X-RAY DIFFRACTION87.57
1.71-1.740.26331720.21262923X-RAY DIFFRACTION87.04
1.74-1.770.26561380.20582950X-RAY DIFFRACTION87.5
1.77-1.80.26071530.20142916X-RAY DIFFRACTION87.59
1.8-1.830.25521550.22889X-RAY DIFFRACTION86.72
1.83-1.870.23091560.19682916X-RAY DIFFRACTION87.55
1.87-1.910.22521710.18722861X-RAY DIFFRACTION86.68
1.91-1.950.24121580.18522909X-RAY DIFFRACTION87.35
1.95-1.990.21841940.18122923X-RAY DIFFRACTION87.9
1.99-2.040.22841360.17632931X-RAY DIFFRACTION87.21
2.04-2.10.21521320.18072913X-RAY DIFFRACTION86.78
2.1-2.160.20531550.17372932X-RAY DIFFRACTION87.62
2.16-2.230.20141630.17032895X-RAY DIFFRACTION86.92
2.23-2.310.20721620.17162875X-RAY DIFFRACTION86.2
2.31-2.40.21611520.1712910X-RAY DIFFRACTION86.33
2.4-2.510.20791540.17542893X-RAY DIFFRACTION86.29
2.51-2.640.22011490.18032870X-RAY DIFFRACTION85.19
2.64-2.810.21551800.17822830X-RAY DIFFRACTION85.12
2.81-3.030.21431640.17552853X-RAY DIFFRACTION85.01
3.03-3.330.2181370.16832820X-RAY DIFFRACTION83.41
3.33-3.810.18981440.16022784X-RAY DIFFRACTION81.81
3.81-4.80.13591300.14692738X-RAY DIFFRACTION80.56
4.8-28.990.19771460.19572583X-RAY DIFFRACTION74.24

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