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- PDB-1n8s: Structure of the pancreatic lipase-colipase complex -

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Basic information

Entry
Database: PDB / ID: 1n8s
TitleStructure of the pancreatic lipase-colipase complex
Components
  • Triacylglycerol lipase, pancreatic
  • colipase II
KeywordsHYDROLASE / pancreas
Function / homology
Function and homology information


positive regulation of triglyceride lipase activity / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / Retinoid metabolism and transport / Digestion of dietary lipid / lipase binding / lipase activity / intestinal cholesterol absorption / triacylglycerol lipase / triglyceride lipase activity ...positive regulation of triglyceride lipase activity / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / Digestion of dietary lipid / Retinoid metabolism and transport / Digestion of dietary lipid / lipase binding / lipase activity / intestinal cholesterol absorption / triacylglycerol lipase / triglyceride lipase activity / response to food / enzyme activator activity / Retinoid metabolism and transport / lipid catabolic process / digestion / response to bacterium / lipid metabolic 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
Colipase / Pancreatic triacylglycerol lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.04 Å
Authorsvan Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
CitationJournal: Nature / Year: 1992
Title: Structure of the pancreatic lipase-procolipase complex
Authors: van Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triacylglycerol lipase, pancreatic
C: colipase II


Theoretical massNumber of molelcules
Total (without water)59,9192
Polymers59,9192
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.3, 80.3, 251.0
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Triacylglycerol lipase, pancreatic / / Pancreatic lipase / PL


Mass: 49573.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Pancreatic juice / Source: (natural) Homo sapiens (human) / References: UniProt: P16233, triacylglycerol lipase
#2: Protein colipase II /


Mass: 10345.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: extracted from pancreas / Source: (natural) Sus scrofa (pig) / References: UniProt: P02703

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaCl-0.2-0.5M, PEG 8000 2%, MES 0.1M, BetaOG beyond CMC, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2-0.5 M11NaCl
22 %PEG800011
30.1 MMES11pH6.0
48 mg/mlHPL11
52.5 mg/mlPCL11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLURE DW3210.98
SYNCHROTRONLURE DW3220.98
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 11, 1991
MARRESEARCH2IMAGE PLATEDec 11, 1991
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MirrorsSINGLE WAVELENGTHMx-ray1
2MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.04→30 Å / Num. all: 17720 / Num. obs: 17720 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.085
Reflection shellResolution: 3.04→3.15 Å / % possible all: 62
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 48860

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Processing

Software
NameClassification
XDSdata scaling
AUTOMARdata reduction
MLPHAREphasing
X-PLORrefinement
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 3.04→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 1114 RANDOM
Rwork0.23 --
obs0.23 17720 -
all-17720 -
Refinement stepCycle: LAST / Resolution: 3.04→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 0 0 4131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0027
X-RAY DIFFRACTIONx_angle_d3.5
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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