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- PDB-6qvs: Unliganded structure of the human wild type Beta-galactoside alph... -

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Basic information

Entry
Database: PDB / ID: 6qvs
TitleUnliganded 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 / apo
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 / regulation of substrate adhesion-dependent cell spreading ...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 / regulation of substrate adhesion-dependent cell spreading / protein O-linked GalNAcylation / Termination of O-glycan biosynthesis / negative regulation of macrophage apoptotic process / Sialic acid metabolism / negative regulation of chemotaxis / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi cisterna membrane / Golgi medial cisterna / humoral immune response / 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 / Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase) / sialyltransferase cstii, chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-galactoside alpha-2,6-sialyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Data collection / Database references / Category: diffrn_source / pdbx_related_exp_data_set / Item: _diffrn_source.pdbx_synchrotron_beamline
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 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.6Aug 7, 2024Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_set_type
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)63,9115
Polymers63,6062
Non-polymers3043
Water7,368409
1
A: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0013
Polymers31,8031
Non-polymers1982
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)31,9092
Polymers31,8031
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.816, 94.369, 64.472
Angle α, β, γ (deg.)90.000, 94.310, 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 366-371 (chain A) and 366-370 (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, EC: 2.4.99.1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.84 % / 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, 8% (w/v) PEG 20.000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→38.04 Å / Num. obs: 107819 / % possible obs: 98.86 % / Redundancy: 5 % / Rmerge(I) obs: 0.0456 / Rpim(I) all: 0.02301 / Rrim(I) all: 0.05124 / Net I/σ(I): 17.43
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6128 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 10784 / Rpim(I) all: 0.3004 / Rrim(I) all: 0.6841 / % possible all: 99.09

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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: 1.6→38.039 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 5389 5 %
Rwork0.1811 102406 -
obs0.1821 107795 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.77 Å2 / Biso mean: 29.3099 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 1.6→38.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 591 409 5393
Biso mean--38.05 36.93 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064618
X-RAY DIFFRACTIONf_angle_d0.7926288
X-RAY DIFFRACTIONf_chiral_restr0.054671
X-RAY DIFFRACTIONf_plane_restr0.006805
X-RAY DIFFRACTIONf_dihedral_angle_d8.8523707
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61820.26551780.2519339199
1.6182-1.63720.26831780.2441338999
1.6372-1.65720.23971830.2386346399
1.6572-1.67820.26961790.2283340999
1.6782-1.70030.26481790.2187338999
1.7003-1.72350.22171780.2166339999
1.7235-1.74820.25231820.2119345499
1.7482-1.77430.2351770.2083335699
1.7743-1.8020.29691800.2287341299
1.802-1.83150.24751800.2088343499
1.8315-1.86310.22821800.2021340099
1.8631-1.8970.22791790.1985343199
1.897-1.93350.2211800.1875340799
1.9335-1.97290.19651800.1885342399
1.9729-2.01580.22721810.195344399
2.0158-2.06270.21831790.1883398100
2.0627-2.11430.21451800.19833423100
2.1143-2.17150.2191800.193431100
2.1715-2.23530.22211820.19733450100
2.2353-2.30750.17231800.1871341999
2.3075-2.390.23021820.1854346099
2.39-2.48560.19661790.1889340899
2.4856-2.59870.21871690.1886321094
2.5987-2.73570.20271660.1762315291
2.7357-2.9070.22281830.18793471100
2.907-3.13140.21011820.18433464100
3.1314-3.44630.17311830.17623469100
3.4463-3.94460.16271830.16223474100
3.9446-4.9680.16371840.13373492100
4.968-38.0390.19011830.1817348599

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