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- PDB-1oqm: A 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltra... -

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Basic information

Entry
Database: PDB / ID: 1oqm
TitleA 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltransferase in the presence of UDP-N-acetyl-galactosamine
Components
  • Alpha-lactalbumin
  • beta-1,4-galactosyltransferase
KeywordsTRANSFERASE / BIOSYNTHETIC PROTEIN / alpha-lactalbumin / beta1 / 4-galactosyltransferase / UDP-GalNAc
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 / Golgi trans cisterna / penetration of zona pellucida / UDP-galactosyltransferase activity / regulation of acrosome reaction / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / development of secondary sexual characteristics / macrophage migration / desmosome / acute inflammatory response / galactose metabolic process / positive regulation of epithelial cell proliferation involved in wound healing / binding of sperm to zona pellucida / protein N-linked glycosylation / angiogenesis involved in wound healing / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / epithelial cell development / beta-tubulin binding / alpha-tubulin binding / extracellular matrix organization / 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 / 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-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / Beta-1,4-galactosyltransferase 1 / Alpha-lactalbumin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure-based design of beta 1,4-galactosyltransferase I (beta 4Gal-T1) with equally efficient N-acetylgalactosaminyltransferase activity: point mutation broadens beta 4Gal-T1 donor specificity.
Authors: Ramakrishnan, B. / Qasba, P.K.
History
DepositionMar 10, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionMar 18, 2003ID: 1L7W
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999The N-terminal of chains B and D contains a 13 amino acid tag.

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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)95,52812
Polymers93,7354
Non-polymers1,7938
Water11,331629
1
A: Alpha-lactalbumin
B: beta-1,4-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9587
Polymers46,8672
Non-polymers1,0915
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)47,5705
Polymers46,8672
Non-polymers7023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.471, 95.677, 100.581
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmolecules A & B and C & D form a 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltransferase

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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: residues 21-143
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 (domestic cattle) / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P08037, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase

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Non-polymers , 5 types, 637 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: 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.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.72 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 5.5
Details: Sodium citrate, PEG4000, pH 5.5, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlGal-T11drop
210 mg/mlalpha-lactalbumin1drop
3100 mM1reservoirNaCl
4100 mMsodium citrate1reservoirpH5.6
512.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 56163 / Num. obs: 56106 / % possible obs: 89.9 % / Observed criterion σ(I): 1 / Redundancy: 2.15 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 2.01 / Num. unique all: 4719 / Rsym value: 0.359 / % possible all: 76
Reflection
*PLUS
Num. obs: 62285 / % possible obs: 90 % / Num. measured all: 120498 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.56 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5707 10.2 %RANDOM
Rwork0.194 ---
obs0.194 56106 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9573 Å2 / ksol: 0.327944 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å22.3 Å2
2--8.29 Å20 Å2
3----8.39 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 96 629 7121
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 900 10.2 %
Rwork0.272 7881 -
obs--84.9 %
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
Refinement
*PLUS
Num. reflection obs: 55765 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.001
X-RAY DIFFRACTIONc_angle_deg0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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