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- PDB-1nhe: Crystal structure of Lactose synthase complex with UDP -

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Basic information

Entry
Database: PDB / ID: 1nhe
TitleCrystal structure of Lactose synthase complex with UDP
Components
  • ALPHA-LACTALBUMIN
  • BETA-1,4-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE ACTIVATOR/TRANSFERASE / lactose synthase / MAD methods / 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 / regulation of acrosome reaction / penetration of zona pellucida / Golgi trans cisterna / lactose synthase activity / macrophage migration / lactose biosynthetic process / oligosaccharide biosynthetic process / development of secondary sexual characteristics / desmosome / acute inflammatory response / positive regulation of epithelial cell proliferation involved in wound healing / galactose metabolic process / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / epithelial cell development / alpha-tubulin binding / cytoskeletal protein binding / extracellular matrix organization / filopodium / epithelial cell proliferation / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / lysozyme activity / 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-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1 / Alpha-lactalbumin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta-1,4-galactosyltransferase
Authors: Ramakrishnan, B. / Qasba, P.K.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJan 7, 2003ID: 1J94
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)96,04410
Polymers94,7674
Non-polymers1,2776
Water5,963331
1
A: ALPHA-LACTALBUMIN
B: BETA-1,4-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0225
Polymers47,3832
Non-polymers6383
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)48,0225
Polymers47,3832
Non-polymers6383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.171, 99.013, 102.382
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein ALPHA-LACTALBUMIN / / LACTALBUMIN / ALPHA


Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: REGULATORY SUBUNIT OF LACTOSE SYNTHASE
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND B FORM FIRST, C AND D SECOND LACTOSE SYNTHASE COMPLEX
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET17A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29752
#2: Protein BETA-1,4-GALACTOSYLTRANSFERASE / E.C.2.4.1.22, E.C.2.4.1.90, E.C.2.4.1.38 / B4GAL-T1 / BETA4GAL-T1 / BETA-1 / 4-GALTASE 1 / BETA-1 / 4-GALACTOSYLTRANSFERASE 1 / UDP-GALACTOSE: ...B4GAL-T1 / BETA4GAL-T1 / BETA-1 / 4-GALTASE 1 / BETA-1 / 4-GALACTOSYLTRANSFERASE 1 / UDP-GALACTOSE:BETA-N-ACETYLGLUCOSAMINE BETA-1 / 4-GALACTOSYLTRANSFERASE 1


Mass: 33367.461 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 130-402
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND B FORM FIRST, C AND D SECOND LACTOSE SYNTHASE COMPLEX
Source: (gene. exp.) Bos taurus (cattle) / 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 , 4 types, 337 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 / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.85 Å3/Da / Density % sol: 56.5 %
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
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlbeta4Gal-T11drop
210 mg/mlLA1drop
3100 mM1reservoirNaCl
4100 mMsodium citrate1reservoirpH5.6
512.5 %(w/v)PEG40001reservoir
6100 mMUDP-Gal1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97894, 0.97855,0.96334
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978941
20.978551
30.963341
ReflectionResolution: 2.5→20 Å / Num. obs: 36774 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 50.5 Å2 / Rsym value: 0.054 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 3540 / Rsym value: 0.36 / % possible all: 71
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 37099 / % possible obs: 98 % / Num. measured all: 110000 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNS1refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.9 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3686 10 %RANDOM
Rwork0.197 ---
obs0.197 36774 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.3987 Å2 / ksol: 0.304138 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-13.26 Å20 Å26.23 Å2
2--1.54 Å20 Å2
3----14.8 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 78 331 6803
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_deg1.6
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_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 626 10.3 %
Rwork0.295 5430 -
obs--98.9 %
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 DIFFRACTION4UDP_PG.PARUDP_PG.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 33047 / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5

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