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- PDB-1lpa: INTERFACIAL ACTIVATION OF THE LIPASE-PROCOLIPASE COMPLEX BY MIXED... -

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Basic information

Entry
Database: PDB / ID: 1lpa
TitleINTERFACIAL ACTIVATION OF THE LIPASE-PROCOLIPASE COMPLEX BY MIXED MICELLES REVEALED BY X-RAY CRYSTALLOGRAPHY
Components
  • COLIPASE
  • LIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


positive regulation of triglyceride lipase activity / Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / lipase activity ...positive regulation of triglyceride lipase activity / Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / lipase activity / intestinal cholesterol absorption / high-density lipoprotein particle remodeling / triacylglycerol lipase / triacylglycerol lipase activity / Developmental Lineage of Pancreatic Acinar Cells / response to food / retinoid metabolic process / Retinoid metabolism and transport / lipid catabolic process / digestion / cholesterol homeostasis / response to bacterium / enzyme activator activity / lipid metabolic process / fatty acid biosynthetic process / 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
DIUNDECYL PHOSPHATIDYL CHOLINE / Colipase / Pancreatic triacylglycerol lipase
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.04 Å
AuthorsVan Tilbeurgh, H. / Egloff, M.-P. / Cambillau, C.
Citation
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.
#1: Journal: To be Published
Title: The 2.46 Angstroms Resolution Structure of the Pancreatic Lipase Colipase Complex Inhibited by a C11 Alkyl Phosphonate
Authors: Egloff, M.-P. / Marguet, F. / Buono, G. / Verger, R. / Cambillau, C. / Van Tilbeurgh, H.
#2: Journal: Nature / Year: 1992
Title: Structure of the Pancreatic Lipase-Procolipase Complex
Authors: Van Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
History
DepositionAug 19, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLIPASE
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8895
Polymers59,9192
Non-polymers9693
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.400, 133.400, 92.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: CIS PROLINE - PRO B 16
2: TRP B 30 - SER B 30A OMEGA = 141.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: SER B 30A - PRO B 31 OMEGA = 285.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO B 211 / 5: CIS PROLINE - PRO B 298

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Components

#1: Protein COLIPASE


Mass: 10345.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P02703
#2: Protein LIPASE


Mass: 49573.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PANCREAS / References: UniProt: P16233, triacylglycerol lipase
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mMphosphatidylcholine1drop
260 mMsodium taurodeoxycholate1drop
38 mg/mlpanvreatic lipase1drop
42.5 mg/mlprocolipase1drop
5250 mMbeta-octylglucoside1drop
60.1 MMES1reservoir
70.3 M1reservoirNaCl
82 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. obs: 15496 / % possible obs: 90 % / Num. measured all: 97990 / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.04→8 Å / Rfactor Rwork: 0.186 / Rfactor obs: 0.186 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 3.04→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 63 0 4195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.6

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