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- PDB-6apj: Crystal Structure of human ST6GALNAC2 -

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Basic information

Entry
Database: PDB / ID: 6apj
TitleCrystal Structure of human ST6GALNAC2
ComponentsAlpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase / alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity / protein sialylation / Maturation of protein 3a / sialyltransferase activity / Maturation of protein 3a / Termination of O-glycan biosynthesis / O-glycan processing / Sialic acid metabolism / protein O-linked glycosylation ...alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase / alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity / protein sialylation / Maturation of protein 3a / sialyltransferase activity / Maturation of protein 3a / Termination of O-glycan biosynthesis / O-glycan processing / Sialic acid metabolism / protein O-linked glycosylation / protein glycosylation / Maturation of spike protein / viral protein processing / Golgi membrane
Similarity search - Function
Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase)
Similarity search - Domain/homology
Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsForouhar, F. / Moremen, K.W. / Northeast Structural Genomics Consortium (NESG) / Tong, L.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Expression system for structural and functional studies of human glycosylation enzymes.
Authors: Moremen, K.W. / Ramiah, A. / Stuart, M. / Steel, J. / Meng, L. / Forouhar, F. / Moniz, H.A. / Gahlay, G. / Gao, Z. / Chapla, D. / Wang, S. / Yang, J.Y. / Prabhakar, P.K. / Johnson, R. / ...Authors: Moremen, K.W. / Ramiah, A. / Stuart, M. / Steel, J. / Meng, L. / Forouhar, F. / Moniz, H.A. / Gahlay, G. / Gao, Z. / Chapla, D. / Wang, S. / Yang, J.Y. / Prabhakar, P.K. / Johnson, R. / Rosa, M.D. / Geisler, C. / Nairn, A.V. / Seetharaman, J. / Wu, S.C. / Tong, L. / Gilbert, H.J. / LaBaer, J. / Jarvis, D.L.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
B: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
C: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
D: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
E: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
F: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,23210
Polymers253,3476
Non-polymers8854
Water00
1
A: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6673
Polymers42,2251
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2


Theoretical massNumber of molelcules
Total (without water)42,2251
Polymers42,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2


Theoretical massNumber of molelcules
Total (without water)42,2251
Polymers42,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2


Theoretical massNumber of molelcules
Total (without water)42,2251
Polymers42,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4462
Polymers42,2251
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4462
Polymers42,2251
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.346, 71.803, 134.246
Angle α, β, γ (deg.)98.78, 101.92, 103.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 / GalNAc alpha-2 / 6-sialyltransferase II / ST6GalNAc II / ST6GalNAcII / SThM / Sialyltransferase 7B / SIAT7-B


Mass: 42224.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST6GALNAC2, SIAT7B, SIATL1, STHM / Plasmid: pGEn2
Details (production host): mammalian expression vector (CMV promoter)
Cell line (production host): HEK293S GNT1- / Production host: Homo sapiens (human)
References: UniProt: Q9UJ37, Transferases; Glycosyltransferases; Transferring other glycosyl groups
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.2
Details: 0.1M Sodium Citrate (pH 4.2), 0.1M Ammonium Sulfate, and 24% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2015 / Details: mirrors
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.1→128.4 Å / Num. obs: 52564 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 91 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Rsym value: 0.083 / Χ2: 1.5 / Net I/av σ(I): 11.4 / Net I/σ(I): 11.4
Reflection shellResolution: 3.1→3.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4117 / Rpim(I) all: 0.416 / Rsym value: 0.588 / Χ2: 0.9 / % possible all: 93.3

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Processing

Software
NameClassification
PHENIXrefinement
REFMACrefinement
CNSrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→44.28 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2523 4185 9.99 %
Rwork0.201 --
obs0.2062 41880 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13883 0 56 0 13939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214354
X-RAY DIFFRACTIONf_angle_d0.50719477
X-RAY DIFFRACTIONf_dihedral_angle_d19.7718332
X-RAY DIFFRACTIONf_chiral_restr0.0412098
X-RAY DIFFRACTIONf_plane_restr0.0042462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.47061480.36911292X-RAY DIFFRACTION96
3.1352-3.17210.35281470.32451257X-RAY DIFFRACTION96
3.1721-3.21080.33121530.29171280X-RAY DIFFRACTION94
3.2108-3.25140.34391480.281248X-RAY DIFFRACTION94
3.2514-3.29420.351540.28231269X-RAY DIFFRACTION93
3.2942-3.33930.32781190.2631143X-RAY DIFFRACTION88
3.3393-3.3870.34521480.26011324X-RAY DIFFRACTION95
3.387-3.43750.3051500.25341309X-RAY DIFFRACTION97
3.4375-3.49120.30281250.25321282X-RAY DIFFRACTION96
3.4912-3.54840.31031440.23671349X-RAY DIFFRACTION96
3.5484-3.60960.27881340.24331275X-RAY DIFFRACTION96
3.6096-3.67520.30181250.2391278X-RAY DIFFRACTION95
3.6752-3.74580.26391450.22881326X-RAY DIFFRACTION96
3.7458-3.82230.29031490.2051244X-RAY DIFFRACTION95
3.8223-3.90530.25871370.19841272X-RAY DIFFRACTION94
3.9053-3.99610.26511250.19761301X-RAY DIFFRACTION93
3.9961-4.0960.25971220.19241189X-RAY DIFFRACTION90
4.096-4.20660.25291430.19231256X-RAY DIFFRACTION91
4.2066-4.33030.27181490.18791243X-RAY DIFFRACTION95
4.3303-4.470.21661560.16651324X-RAY DIFFRACTION95
4.47-4.62960.2061310.1611251X-RAY DIFFRACTION95
4.6296-4.81470.19541350.15411272X-RAY DIFFRACTION94
4.8147-5.03350.19521370.15831238X-RAY DIFFRACTION92
5.0335-5.29850.21911410.16851232X-RAY DIFFRACTION91
5.2985-5.62990.23781300.1841193X-RAY DIFFRACTION88
5.6299-6.06360.22561410.1961272X-RAY DIFFRACTION94
6.0636-6.67190.24441280.19011257X-RAY DIFFRACTION92
6.6719-7.63310.25071360.19261192X-RAY DIFFRACTION89
7.6331-9.60070.18351380.16511172X-RAY DIFFRACTION87
9.6007-44.28430.26121470.21221155X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -8.1163 Å / Origin y: 7.2187 Å / Origin z: 31.7724 Å
111213212223313233
T0.3545 Å2-0.0489 Å2-0.0108 Å2-0.3571 Å2-0.0208 Å2--0.3639 Å2
L0.1387 °2-0.1249 °20.0022 °2-0.1267 °2-0.0318 °2--0.2005 °2
S0.0203 Å °-0.0316 Å °0.0089 Å °-0.0725 Å °0.0037 Å °-0.0314 Å °0.1406 Å °-0.1567 Å °0.018 Å °
Refinement TLS groupSelection details: all

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