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- PDB-6qvt: CMP-Sialic acid bound structure of the human wild type Beta-galac... -

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Basic information

Entry
Database: PDB / ID: 6qvt
TitleCMP-Sialic acid bound structure of the human wild type Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6Gal1)
ComponentsBeta-galactoside alpha-2,6-sialyltransferase 1
KeywordsTRANSFERASE / Sialyltransferase / Beta-galactoside alpha-2 / 6-sialyltransferase 1 / ST6Gal1 / N-linked glycosylation / CMP-Sia / Sialic acid / Cytidine-5'-monophospho-N-acetylneuraminic / CMP-Neu5Ac / CMP-Sialic acid
Function / homology
Function and homology information


beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / Termination of O-glycan biosynthesis ...beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / Termination of O-glycan biosynthesis / regulation of substrate adhesion-dependent cell spreading / negative regulation of chemotaxis / O-glycan processing / Sialic acid metabolism / negative regulation of macrophage apoptotic process / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi cisterna membrane / humoral immune response / Golgi medial cisterna / Maturation of spike protein / response to ethanol / viral protein processing / Golgi membrane / Golgi apparatus / protein homodimerization activity / extracellular region
Similarity search - Function
Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase)
Similarity search - Domain/homology
Chem-NCC / DI(HYDROXYETHYL)ETHER / Beta-galactoside alpha-2,6-sialyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHarrus, D. / Glumoff, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland285232 Finland
Citation
Journal: J.Struct.Biol. / Year: 2020
Title: Unliganded and CMP-Neu5Ac bound structures of human alpha-2,6-sialyltransferase ST6Gal I at high resolution.
Authors: Harrus, D. / Harduin-Lepers, A. / Glumoff, T.
#1: Journal: J.Struct.Biol. / Year: 2020
Title: Unliganded and CMP-Neu5Ac bound structures of human alpha-2,6-sialyltransferase ST6Gal I at high resolution
Authors: Harrus, D. / Harduin-Lepers, A. / Glumoff, T.
History
DepositionMar 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 19, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.4Oct 7, 2020Group: Database references / Category: citation / citation_author
Revision 1.5Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactoside alpha-2,6-sialyltransferase 1
B: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0476
Polymers63,6062
Non-polymers1,4414
Water4,612256
1
A: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5243
Polymers31,8031
Non-polymers7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5243
Polymers31,8031
Non-polymers7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.661, 93.921, 63.718
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-galactoside alpha-2,6-sialyltransferase 1 / / Alpha 2 / 6-ST 1 / B-cell antigen CD75 / CMP-N-acetylneuraminate-beta-galactosamide-alpha-2 / 6- ...Alpha 2 / 6-ST 1 / B-cell antigen CD75 / CMP-N-acetylneuraminate-beta-galactosamide-alpha-2 / 6-sialyltransferase 1 / ST6Gal I / ST6GalI / Sialyltransferase 1


Mass: 31803.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Compound details: residues 365-371 (chain A) and 132-135, 366-371 (chain B) did not have clear electron density and were not traced
Source: (gene. exp.) Homo sapiens (human) / Gene: ST6GAL1, SIAT1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15907, beta-galactoside alpha-(2,6)-sialyltransferase
#2: Chemical ChemComp-NCC / CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID


Mass: 614.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31N4O16P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.21 Å3/Da / Density % sol: 61.62 % / Description: 30-100 um prism-shaped plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.7→48.346 Å / Num. obs: 104377 / % possible obs: 98.73 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.0419 / Rpim(I) all: 0.02626 / Rrim(I) all: 0.04958 / Net I/σ(I): 13.87
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6138 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10330 / Rpim(I) all: 0.3763 / Rrim(I) all: 0.7214 / % possible all: 97.78

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JS1

4js1


Resolution: 1.7→48.346 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 4361 5 %
Rwork0.1817 82812 -
obs0.1828 87173 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.38 Å2 / Biso mean: 35.2105 Å2 / Biso min: 15.48 Å2
Refinement stepCycle: final / Resolution: 1.7→48.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 178 258 4783
Biso mean--36.78 42.85 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064722
X-RAY DIFFRACTIONf_angle_d0.8136455
X-RAY DIFFRACTIONf_chiral_restr0.052700
X-RAY DIFFRACTIONf_plane_restr0.006806
X-RAY DIFFRACTIONf_dihedral_angle_d7.6993793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.32191460.2974276098
1.7193-1.73950.32411430.2731272398
1.7395-1.76080.28111440.2629274799
1.7608-1.78310.26361420.2508268298
1.7831-1.80650.24341470.2416279199
1.8065-1.83130.24231430.2305271098
1.8313-1.85740.24821440.2182273499
1.8574-1.88520.25221450.2133275497
1.8852-1.91460.22571430.2009272499
1.9146-1.9460.24461450.1956274999
1.946-1.97960.22921450.1849275599
1.9796-2.01560.2251450.1846274699
2.0156-2.05430.25011460.1807277399
2.0543-2.09630.1981420.1858271099
2.0963-2.14180.22081480.1792280699
2.1418-2.19170.17841460.1803276999
2.1917-2.24650.1971450.18182761100
2.2465-2.30720.23371470.1802278699
2.3072-2.37510.21131440.1852274799
2.3751-2.45180.17381480.17832797100
2.4518-2.53940.21251450.18652758100
2.5394-2.6410.18631460.1733277499
2.641-2.76120.19741470.1651280099
2.7612-2.90680.18131450.1732274199
2.9068-3.08890.21271440.1718275399
3.0889-3.32730.18561470.1728278399
3.3273-3.66210.19631460.1611276999
3.6621-4.19170.18871470.1605279199
4.1917-5.28010.17751470.1652279499
5.2801-48.3460.21211490.2073282598

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