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- PDB-3ee5: Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I ... -

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Basic information

Entry
Database: PDB / ID: 3ee5
TitleCrystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / Closed conformation / carbohydrate acceptor binding / Alternative initiation / Cell membrane / Congenital disorder of glycosylation / Glycoprotein / Glycosyltransferase / Golgi apparatus / Manganese / Membrane / Metal-binding / Secreted / Signal-anchor / Transmembrane
Function / homology
Function and homology information


Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / penetration of zona pellucida / Lactose synthesis / regulation of acrosome reaction / Keratan sulfate biosynthesis / 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 / N-Glycan antennae elongation / UDP-galactosyltransferase activity / Golgi trans cisterna / macrophage migration / lactose synthase activity / development of secondary sexual characteristics / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / acute inflammatory response / galactose metabolic process / positive regulation of epithelial cell proliferation involved in wound healing / Pre-NOTCH Processing in Golgi / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / azurophil granule membrane / Golgi cisterna membrane / epithelial cell development / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / extracellular matrix organization / secretory granule membrane / epithelial cell proliferation / filopodium / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / external side of plasma membrane / Golgi membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
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
naphthalen-2-ylmethanol / 1,4-DIETHYLENE DIOXIDE / : / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Deoxygenated Disaccharide Analogs as Specific Inhibitors of {beta}1-4-Galactosyltransferase 1 and Selectin-mediated Tumor Metastasis
Authors: Brown, J.R. / Yang, F. / Sinha, A. / Ramakrishnan, B. / Tor, Y. / Qasba, P.K. / Esko, J.D.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
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_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,89238
Polymers98,3203
Non-polymers5,57235
Water8,557475
1
A: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,53812
Polymers32,7731
Non-polymers1,76411
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)34,91416
Polymers32,7731
Non-polymers2,14115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44110
Polymers32,7731
Non-polymers1,6679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.127, 195.742, 143.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Beta-1,4-galactosyltransferase 1 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4- ...Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4-galactosyltransferase 1 / UDP-Gal:beta-GlcNAc beta-1 / 4-galactosyltransferase 1


Mass: 32773.230 Da / Num. of mol.: 3
Fragment: Catalytic domain of Beta-1,4-Galactosyltransferase
Mutation: d126, M340H, C338T, R337T
Source method: isolated from a genetically manipulated source
Details: Expressed with a 14 amino acid N-terminal tag from the vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: B4GALT1, GGTB2 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P15291, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 507 molecules

#3: Chemical ChemComp-UDH / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE


Mass: 503.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H27N3O12P2
#4: Chemical ChemComp-2NA / naphthalen-2-ylmethanol / Naphthalenemethanol


Mass: 158.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H10O
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: MES, AMMONIUM SULFATE, DIOXANE, pH 6.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 2006 / Details: mirros
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 85066 / Num. obs: 85066 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 16.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 7523 / Rsym value: 0.546 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AEC

2aec


Resolution: 2.2→46.33 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3004894.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 7621 10.1 %RANDOM
Rwork0.206 ---
obs0.206 75540 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8241 Å2 / ksol: 0.353855 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.77 Å20 Å20 Å2
2--15.47 Å20 Å2
3----11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 340 475 7469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 1275 10.4 %
Rwork0.275 10974 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4udph_ctb1.parudph_ctb1.top

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