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- PDB-1eth: TRIACYLGLYCEROL LIPASE/COLIPASE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1eth
TitleTRIACYLGLYCEROL LIPASE/COLIPASE COMPLEX
Components
  • COLIPASE
  • TRIACYLGLYCEROL ACYL-HYDROLASE
KeywordsCOMPLEX (HYDROLASE/COFACTOR) / COMPLEX (HYDROLASE-COFACTOR) / LIPID DEGRADATION / COMPLEX (HYDROLASE-COFACTOR) complex
Function / homology
Function and homology information


Digestion of dietary lipid / Retinoid metabolism and transport / lipase binding / lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / response to food / lipid catabolic process / enzyme activator activity / digestion ...Digestion of dietary lipid / Retinoid metabolism and transport / lipase binding / lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / response to food / lipid catabolic process / enzyme activator activity / digestion / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase ...Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase / Pancreatic lipase / Lipase, subunit A / Lipase, subunit A / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Pancreatic triacylglycerol lipase / Colipase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHermoso, J. / Pignol, D. / Kerfelec, B. / Crenon, I. / Chapus, C. / Fontecilla-Camps, J.C.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Lipase activation by nonionic detergents. The crystal structure of the porcine lipase-colipase-tetraethylene glycol monooctyl ether complex.
Authors: Hermoso, J. / Pignol, D. / Kerfelec, B. / Crenon, I. / Chapus, C. / Fontecilla-Camps, J.C.
#1: Journal: Nature / Year: 1993
Title: Interfacial Activation of the Lipase-Procolipase Complex by Mixed Micelles Revealed by X-Ray Crystallography
Authors: Van Tilbeurgh, H. / Egloff, M.P. / Martinez, C. / Rugani, N. / Verger, R. / Cambillau, C.
#2: Journal: Nature / Year: 1992
Title: Structure of the Pancreatic Lipase-Procolipase Complex
Authors: Van Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
History
DepositionSep 13, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIACYLGLYCEROL ACYL-HYDROLASE
B: COLIPASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
D: COLIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,74114
Polymers120,4574
Non-polymers3,28410
Water6,431357
1
A: TRIACYLGLYCEROL ACYL-HYDROLASE
B: COLIPASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,42113
Polymers110,1373
Non-polymers3,28410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRIACYLGLYCEROL ACYL-HYDROLASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
D: COLIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,42113
Polymers110,1373
Non-polymers3,28410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)289.100, 289.100, 289.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein TRIACYLGLYCEROL ACYL-HYDROLASE / TRIACYLGLYCEROL LIPASE


Mass: 49908.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00591, triacylglycerol lipase
#2: Protein COLIPASE


Mass: 10319.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P02703

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Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 365 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 61 %
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mllipase1drop0.01ml
210 mg/mlcolipase1drop0.007 ml
350 mMMES1reservoir
40.5 Mammonium sulfate1reservoir
515 mMTGME1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorDetector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→12.4 Å / Num. obs: 42501 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.8→6 Å / σ(F): 2 / Details: CRYST1 UNUSUAL UNIT-CELL DATA: PSEUDOSYMMETRY P 23
RfactorNum. reflection% reflection
Rfree0.29 -7 %
Rwork0.21 --
obs0.21 33758 -
Displacement parametersBiso mean: 19.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 216 357 8911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.62

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