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- PDB-1o23: CRYSTAL STRUCTURE OF LACTOSE SYNTHASE IN THE PRESENCE OF UDP-GLUCOSE -

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Basic information

Entry
Database: PDB / ID: 1o23
TitleCRYSTAL STRUCTURE OF LACTOSE SYNTHASE IN THE PRESENCE OF UDP-GLUCOSE
Components
  • ALPHA-LACTALBUMIN
  • BETA-1,4-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE ACTIVATOR/TRANSFERASE / ALPHA-LACTALBUMIN / BETA / 1 / 4-GALACTOSYLTRANSFERASE / UDP-GLUCOSE / TRANSFERASE ACTIVATOR-TRANSFERASE COMPLEX
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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 / lysozyme activity / manganese ion binding / basolateral plasma membrane / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / external side of plasma membrane / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Lactalbumin / 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 / Lysozyme - #10 ...Lactalbumin / 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 / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Beta-1,4-galactosyltransferase 1 / Alpha-lactalbumin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRamakrishnan, B. / Shah, P.S. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Alpha-Lactalbumin (La) Stimulates Milk Beta-1,4-Galactosyltransferase I (Beta 4Gal-T1) to Transfer Glucose from Udp-Glucose to N-Acetylglucosamine. Crystal Structure of Beta 4Gal-T1 X La Complex with Udp-Glc.
Authors: Ramakrishnan, B. / Shah, P.S. / Qasba, P.K.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 25, 2003ID: 1NT7
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2013Group: Non-polymer description
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LACTALBUMIN
B: BETA-1,4-GALACTOSYLTRANSFERASE
C: ALPHA-LACTALBUMIN
D: BETA-1,4-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,45015
Polymers93,7354
Non-polymers2,71511
Water7,422412
1
A: ALPHA-LACTALBUMIN
B: BETA-1,4-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3228
Polymers46,8672
Non-polymers1,4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ALPHA-LACTALBUMIN
D: BETA-1,4-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1277
Polymers46,8672
Non-polymers1,2605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.545, 99.379, 102.568
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein ALPHA-LACTALBUMIN / LACTOSE SYNTHASE B PROTEIN


Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: REGULATORY SUBUNIT OF LACTOSE SYNTHASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LALBA / Plasmid: PET17.1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29752
#2: Protein BETA-1,4-GALACTOSYLTRANSFERASE


Mass: 32851.617 Da / Num. of mol.: 2 / Fragment: RESIDUES 57-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BETA1,4-GALACTOSYLTRANSFERASE / Plasmid: PET23C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08037, N-acetyllactosamine synthase

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Non-polymers , 7 types, 423 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.81 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium citrate, PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2000 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.28→20 Å / Num. all: 47286 / Num. obs: 46829 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 14.8
Reflection shellResolution: 2.28→2.37 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 4972 / Rsym value: 0.61 / % possible all: 91

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1292941.44 / Data cutoff high rms absF: 1292941.44 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4654 10.1 %RANDOM
Rwork0.201 ---
obs0.201 46195 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.85 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å22.98 Å2
2--16.96 Å20 Å2
3----16.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-8 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.32→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 164 412 6972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 780 10.1 %
Rwork0.301 6911 -
obs--99.6 %
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_PG.PARUDPG_PG.TOP
X-RAY DIFFRACTION5

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