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- PDB-4cj8: monoclinic crystal form of Bogt6a E192Q in complex with UDP-GalNA... -

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Basic information

Entry
Database: PDB / ID: 4cj8
Titlemonoclinic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP and GalNAc
ComponentsGLYCOSYLTRANSFERASE FAMILY 6
KeywordsTRANSFERASE / MONOCLINIC FORM / METAL-INDEPENDENT / HYDROLYSED PRODUCTS
Function / homology
Function and homology information


hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / membrane / metal ion binding
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 / 2-acetamido-2-deoxy-beta-D-galactopyranose / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase family 6
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 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_conn / 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 / _struct_conn.pdbx_leaving_atom_flag
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
E: GLYCOSYLTRANSFERASE FAMILY 6
F: GLYCOSYLTRANSFERASE FAMILY 6
G: GLYCOSYLTRANSFERASE FAMILY 6
H: GLYCOSYLTRANSFERASE FAMILY 6
I: GLYCOSYLTRANSFERASE FAMILY 6
J: GLYCOSYLTRANSFERASE FAMILY 6
K: GLYCOSYLTRANSFERASE FAMILY 6
L: GLYCOSYLTRANSFERASE FAMILY 6
M: GLYCOSYLTRANSFERASE FAMILY 6
N: GLYCOSYLTRANSFERASE FAMILY 6
O: GLYCOSYLTRANSFERASE FAMILY 6
P: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,88949
Polymers468,19716
Non-polymers10,69333
Water1267
1
B: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9844
Polymers29,2621
Non-polymers7213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9804
Polymers29,2621
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,2621
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,2621
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
H: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,2621
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
J: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
K: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
L: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
N: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
O: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,2621
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
A: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3106
Polymers29,2621
Non-polymers1,0485
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
C: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
G: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers29,2621
Non-polymers7923
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
I: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
M: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8883
Polymers29,2621
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: GLYCOSYLTRANSFERASE FAMILY 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8702
Polymers29,2621
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.690, 79.740, 179.080
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
GLYCOSYLTRANSFERASE FAMILY 6 / GLYCOSYLTRANSFERASE


Mass: 29262.297 Da / Num. of mol.: 16 / Fragment: ACTIVE SITE, RESIDUES 1-246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7LVT2, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase

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Sugars , 2 types, 10 molecules

#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 / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 8
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
#8: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


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

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Non-polymers , 6 types, 30 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: 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.: 6 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.5 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 5 / Details: 0.2M 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 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→87.98 Å / Num. obs: 61949 / % possible obs: 98 % / Observed criterion σ(I): 7.4 / Redundancy: 2.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.4
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 4CJB

4cjb


Resolution: 3.5→87.977 Å / σ(F): 1.34 / Phase error: 28.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2494 3254 5.2 %
Rwork0.2253 --
obs0.2266 61938 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→87.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32187 0 683 7 32877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233943
X-RAY DIFFRACTIONf_angle_d0.52946150
X-RAY DIFFRACTIONf_dihedral_angle_d11.51812600
X-RAY DIFFRACTIONf_chiral_restr0.0234728
X-RAY DIFFRACTIONf_plane_restr0.0035809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5003-3.56060.33571550.28562909X-RAY DIFFRACTION94
3.5606-3.62530.30331400.283010X-RAY DIFFRACTION94
3.6253-3.6950.28581520.25772915X-RAY DIFFRACTION94
3.695-3.77040.28561670.25132934X-RAY DIFFRACTION93
3.7704-3.85240.29031900.24922897X-RAY DIFFRACTION92
3.8524-3.9420.27941250.24262959X-RAY DIFFRACTION94
3.942-4.04050.30771560.23342940X-RAY DIFFRACTION94
4.0405-4.14970.25571460.22822940X-RAY DIFFRACTION94
4.1497-4.27170.25561570.22462943X-RAY DIFFRACTION93
4.2717-4.40950.23891860.21042902X-RAY DIFFRACTION92
4.4095-4.5670.21371600.19782916X-RAY DIFFRACTION93
4.567-4.74960.23191760.19722929X-RAY DIFFRACTION92
4.7496-4.96560.23621430.20482973X-RAY DIFFRACTION93
4.9656-5.22710.22771590.2112905X-RAY DIFFRACTION93
5.2271-5.55410.26461570.21922928X-RAY DIFFRACTION93
5.5541-5.98220.26461610.23822936X-RAY DIFFRACTION92
5.9822-6.58270.2831610.23292948X-RAY DIFFRACTION92
6.5827-7.53190.24411550.22042937X-RAY DIFFRACTION92
7.5319-9.47690.21281640.19652915X-RAY DIFFRACTION91
9.4769-47.25150.18491270.21473028X-RAY DIFFRACTION91

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