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- PDB-4mps: Crystal structure of rat Beta-galactoside alpha-2,6-sialyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4mps
TitleCrystal structure of rat Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1), Northeast Structural Genomics Consortium Target RnR367A
ComponentsBeta-galactoside alpha-2,6-sialyltransferase 1
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / Beta-galactoside alpha-2 / 6-sialyltransferase 1
Function / homology
Function and homology information


Sialic acid metabolism / N-Glycan antennae elongation / Termination of O-glycan biosynthesis / beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Golgi trans cisterna / regulation of substrate adhesion-dependent cell spreading ...Sialic acid metabolism / N-Glycan antennae elongation / Termination of O-glycan biosynthesis / beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Golgi trans cisterna / regulation of substrate adhesion-dependent cell spreading / negative regulation of macrophage apoptotic process / negative regulation of chemotaxis / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi medial cisterna / Golgi cisterna membrane / protein glycosylation / response to ethanol / 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
Beta-galactoside alpha-2,6-sialyltransferase 1 / Beta-galactoside alpha-2,6-sialyltransferase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsForouhar, F. / Meng, L. / Milaninia, S. / Seetharaman, J. / Su, M. / Kornhaber, G. / Montelione, G.T. / Hunt, J.F. / Moremen, K.W. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Enzymatic Basis for N-Glycan Sialylation: STRUCTURE OF RAT alpha 2,6-SIALYLTRANSFERASE (ST6GAL1) REVEALS CONSERVED AND UNIQUE FEATURES FOR GLYCAN SIALYLATION.
Authors: Meng, L. / Forouhar, F. / Thieker, D. / Gao, Z. / Ramiah, A. / Moniz, H. / Xiang, Y. / Seetharaman, J. / Milaninia, S. / Su, M. / Bridger, R. / Veillon, L. / Azadi, P. / Kornhaber, G. / ...Authors: Meng, L. / Forouhar, F. / Thieker, D. / Gao, Z. / Ramiah, A. / Moniz, H. / Xiang, Y. / Seetharaman, J. / Milaninia, S. / Su, M. / Bridger, R. / Veillon, L. / Azadi, P. / Kornhaber, G. / Wells, L. / Montelione, G.T. / Woods, R.J. / Tong, L. / Moremen, K.W.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)74,1376
Polymers73,2532
Non-polymers8854
Water3,765209
1
A: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers36,6261
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0693
Polymers36,6261
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.720, 49.754, 86.063
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-galactoside alpha-2,6-sialyltransferase 1 / RCG36561 / isoform CRA_a


Mass: 36626.277 Da / Num. of mol.: 2 / Fragment: UNP residues 95-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: BN / Gene: rCG_36561, St6gal1 / Plasmid: pGEn2 mammalian expression vector / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: G3V680, UniProt: P13721*PLUS, EC: 2.4.99.1
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 37.47 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8
Details: 0.1M Lithium Bromide, 0.1M Tris, pH 8, 40% (v/w) PEG 1000., micro batch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 29, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.4→46.7 Å / Num. all: 44235 / Num. obs: 43837 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.089 / Net I/σ(I): 10.71
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.46 / Num. unique all: 4401 / Rsym value: 0.442 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.3refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 167096.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3985 9.8 %RANDOM
Rwork0.2 ---
all0.198 43671 --
obs0.2 40789 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3879 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.41 Å2
2--0.34 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 56 209 4910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 601 9.5 %
Rwork0.254 5701 -
obs-5701 86.9 %

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