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- PDB-4cjc: orthorhombic crystal form of Bogt6a E192Q in complex with UDP-Gal... -

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Basic information

Entry
Database: PDB / ID: 4cjc
Titleorthorhombic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP, GalNAc
ComponentsGLYCOSYLTRANSFERASE FAMILY 6
KeywordsTRANSFERASE / ORTHORHOMBIC FORM / METAL-INDEPENDENT / HYDROLYSED PRODUCTS
Function / homology
Function and homology information


hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / metal ion binding / membrane
Similarity search - Function
: / Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase family 6
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsPham, T. / Stinson, B. / Thiyagarajan, N. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structures of Complexes of a Metal-Independent Glycosyltransferase Gt6 from Bacteroides Ovatus with Udp-Galnac and its Hydrolysis Products.
Authors: Pham, T.T.K. / Stinson, B. / Thiyagarajan, N. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R.
History
DepositionDec 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOSYLTRANSFERASE FAMILY 6
B: GLYCOSYLTRANSFERASE FAMILY 6
C: GLYCOSYLTRANSFERASE FAMILY 6
D: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,61410
Polymers116,1484
Non-polymers2,4656
Water00
1
A: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6442
Polymers29,0371
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6623
Polymers29,0371
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6442
Polymers29,0371
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6623
Polymers29,0371
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.120, 120.150, 131.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GLYCOSYLTRANSFERASE FAMILY 6 / GLYCOSYLTRANSFERASE


Mass: 29037.072 Da / Num. of mol.: 4 / Fragment: ACTIVE SITE, RESIDUES 1-246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Plasmid: PET42B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7LVT2, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsWITH HIS-TAG

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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: 3.42 Å3/Da / Density % sol: 56.09 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.2 M LI2SO4, 0.1M BIS TRIS, PH 5.5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 289.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 3, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.42→88.8 Å / Num. obs: 17402 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 91.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 3.42→3.51 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CJB

4cjb


Resolution: 3.42→88.802 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 33.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3141 876 5.1 %
Rwork0.2835 --
obs0.2851 17264 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.25 Å2
Refinement stepCycle: LAST / Resolution: 3.42→88.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7962 0 158 0 8120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068388
X-RAY DIFFRACTIONf_angle_d1.20611413
X-RAY DIFFRACTIONf_dihedral_angle_d16.6023107
X-RAY DIFFRACTIONf_chiral_restr0.0541170
X-RAY DIFFRACTIONf_plane_restr0.0081439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4201-3.63440.44731430.3732766X-RAY DIFFRACTION100
3.6344-3.91510.42971480.38672316X-RAY DIFFRACTION85
3.9151-4.3090.34121430.2992752X-RAY DIFFRACTION99
4.309-4.93250.27941400.2512793X-RAY DIFFRACTION100
4.9325-6.21420.32211600.26632809X-RAY DIFFRACTION99
6.2142-88.83150.24091420.25342952X-RAY DIFFRACTION99

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