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- PDB-1tvy: beta-1,4-galactosyltransferase mutant Met344His (M344H-Gal-T1) co... -

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Basic information

Entry
Database: PDB / ID: 1tvy
Titlebeta-1,4-galactosyltransferase mutant Met344His (M344H-Gal-T1) complex with UDP-galactose and manganese
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / Met344His mutantion / closed conformation / Mn binding
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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / : / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRamakrishnan, B. / Boeggeman, E. / Qasba, P.K.
CitationJournal: Biochemistry / Year: 2004
Title: Effect of the Met344His mutation on the conformational dynamics of bovine beta-1,4-galactosyltransferase: crystal structure of the Met344His mutant in complex with chitobiose
Authors: Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,82314
Polymers65,7132
Non-polymers2,11012
Water9,116506
1
A: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9617
Polymers32,8571
Non-polymers1,1056
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)33,8627
Polymers32,8571
Non-polymers1,0056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.476, 93.894, 145.054
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 , 1 types, 2 molecules AB

#1: Protein Beta-1,4-galactosyltransferase 1 / E.C.2.4.1.22, E.C.2.4.1.90, E.C.2.4.1.38 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1


Mass: 32856.531 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: d129, Cys342Thr and Met344His
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle)
Description: N-terminal 13 amino acids belong to T7-tag from the vector
Gene: B4GALT1 / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P08037, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase

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Non-polymers , 5 types, 518 molecules

#2: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mes-NaOH, Ammonium sulfate, dioxane, 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: X9B / Wavelength: 0.9807 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 46763 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.048 / Net I/σ(I): 34
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 10 / Rsym value: 0.172 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O0R

1o0r


Resolution: 2.3→26.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2325447.92 / 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
Rfree0.246 3146 10 %RANDOM
Rwork0.194 ---
all0.1941 31339 --
obs0.1941 31339 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4508 Å2 / ksol: 0.321287 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2--4.74 Å20 Å2
3----7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.26 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 121 506 5069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 519 10.2 %
Rwork0.191 4592 -
obs--100 %
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 DIFFRACTION4UDPG.PARUDPG.TOP

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