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- PDB-4krv: Crystal structure of catalytic domain of bovine beta1,4-galactosy... -

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Basic information

Entry
Database: PDB / ID: 4krv
TitleCrystal structure of catalytic domain of bovine beta1,4-galactosyltransferase mutant M344H-GalT1 complex with 6-sulfo-GlcNAc
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / mutant enzyme / GT-A fold / glycosyltransferase / UDP-galactose / N-acetyl-glucosamine / Golgi
Function / homology
Function and homology information


protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity ...protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / brush border membrane / lipid metabolic process / manganese ion binding / basolateral plasma membrane / external side of plasma membrane / Golgi apparatus / extracellular space / identical protein binding
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / 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
: / Chem-NGS / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Placement / Resolution: 2.4 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: Glycoconj J / Year: 2013
Title: Investigations on beta 1,4-galactosyltransferase I using 6-sulfo-GlcNAc as an acceptor sugar substrate.
Authors: Ramakrishnan, B. / Moncrief, A.J. / Davis, T.A. / Holland, L.A. / Qasba, P.K.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...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
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: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,39318
Polymers65,7132
Non-polymers2,68016
Water2,612145
1
A: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,29210
Polymers32,8571
Non-polymers1,4369
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1008
Polymers32,8571
Non-polymers1,2447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.282, 88.903, 139.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-1,4-galactosyltransferase 1 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1


Mass: 32856.531 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, UNP residues 130-402 / Mutation: M344H, C342T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: B4GALT1, GALT, GGTB2 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P08037, lactose synthase
#4: Sugar ChemComp-NGS / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-SULFATE / N-acetyl-6-O-sulfo-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO9S
IdentifierTypeProgram
DGlcpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 159 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDH / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE


Mass: 503.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27N3O12P2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Mes buffer, 1.8 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 22409 / Num. obs: 22368 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rsym value: 0.106 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4 / Num. unique all: 2262 / Rsym value: 0.438 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: Molecular Placement
Starting model: pdb entry 1TW5

1tw5


Resolution: 2.4→24.641 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1154 5.16 %random
Rwork0.1878 ---
obs0.191 22368 89.93 %-
all-22409 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→24.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 154 145 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044735
X-RAY DIFFRACTIONf_angle_d0.6956443
X-RAY DIFFRACTIONf_dihedral_angle_d14.0341772
X-RAY DIFFRACTIONf_chiral_restr0.05670
X-RAY DIFFRACTIONf_plane_restr0.003816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50490.31061270.23152656X-RAY DIFFRACTION91
2.5049-2.63680.32081430.22472661X-RAY DIFFRACTION92
2.6368-2.80180.31961400.22342680X-RAY DIFFRACTION92
2.8018-3.01770.29041400.21582667X-RAY DIFFRACTION91
3.0177-3.32080.24571670.20942633X-RAY DIFFRACTION90
3.3208-3.79980.26141530.17312633X-RAY DIFFRACTION90
3.7998-4.78160.18631460.14662613X-RAY DIFFRACTION88
4.7816-24.6410.21531380.1752671X-RAY DIFFRACTION85

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