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- PDB-1aql: CRYSTAL STRUCTURE OF BOVINE BILE-SALT ACTIVATED LIPASE COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1aql
TitleCRYSTAL STRUCTURE OF BOVINE BILE-SALT ACTIVATED LIPASE COMPLEXED WITH TAUROCHOLATE
ComponentsBILE-SALT ACTIVATED LIPASE
KeywordsHYDROLASE / SERINE ESTERASE / LIPID DEGRADATION / GLYCOPROTEIN
Function / homologyCarboxylesterases type-B signature 2. / Carboxylesterases type-B serine active site. / Carboxylesterase family / Bile salt-activated lipase / Alpha/Beta hydrolase fold / Carboxylesterase type B, active site / Carboxylesterase type B, conserved site / Carboxylesterase, type B / sterol esterase / sterol esterase activity ...Carboxylesterases type-B signature 2. / Carboxylesterases type-B serine active site. / Carboxylesterase family / Bile salt-activated lipase / Alpha/Beta hydrolase fold / Carboxylesterase type B, active site / Carboxylesterase type B, conserved site / Carboxylesterase, type B / sterol esterase / sterol esterase activity / postsynaptic membrane assembly / neurexin family protein binding / presynaptic membrane assembly / neuron cell-cell adhesion / triacylglycerol lipase / triglyceride lipase activity / synaptic vesicle endocytosis / presynapse / modulation of chemical synaptic transmission / lipid catabolic process / signaling receptor activity / synapse / integral component of plasma membrane / cell surface / extracellular region / cytoplasm / Bile salt-activated lipase
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.8 Å resolution
AuthorsWang, X. / Zhang, X.
CitationJournal: Structure / Year: 1997
Title: The crystal structure of bovine bile salt activated lipase: insights into the bile salt activation mechanism.
Authors: Wang, X. / Wang, C.S. / Tang, J. / Dyda, F. / Zhang, X.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 30, 1997 / Release: Aug 5, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 5, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Aug 24, 2011Structure modelOther
1.4Mar 7, 2018Structure modelData collection / Otherdiffrn_source / pdbx_database_status_diffrn_source.source / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BILE-SALT ACTIVATED LIPASE
B: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6368
Polyers118,1312
Non-polymers2,5056
Water0
1
A: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3184
Polyers59,0651
Non-polymers1,2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3184
Polyers59,0651
Non-polymers1,2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)130.230, 104.090, 120.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide BILE-SALT ACTIVATED LIPASE / CARBOXYL ESTER LIPASE / STEROL ESTERASE / CHOLESTEROL ESTERASE / PANCREATIC LYSOPHOSPHOLIPASE


Mass: 59065.461 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: PANCREAS / References: UniProt: P30122, sterol esterase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 4 / Formula: C26H45NO7S / Taurocholic acid

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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: 3.2 / Density percent sol: 61.5 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
112.5 mg/mlprotein1drop
20.9 Mammonium sulfate1drop
32.5 %isopropanol1drop
40.5 mMTC1drop
50.05 mMsucrose monolaurate1drop
61.8 Mammonium sulfate1reservoir
75 %isopropanol1reservoir
81 mMTC1reservoir
90.1 mMsucrose monolaurate1reservoir

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Data collection

DiffractionMean temperature: 293 kelvins
SourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Collection date: Mar 1, 1997
RadiationMonochromator: CRYSTAL / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 43.5 Å2 / D resolution high: 2.8 Å / D resolution low: 17 Å / Number obs: 33877 / Observed criterion sigma I: 0.5 / Rsym value: 0.117 / NetI over sigmaI: 9.1 / Redundancy: 1.8 % / Percent possible obs: 82.7
Reflection shellHighest resolution: 2.8 Å / Lowest resolution: 2.9 Å / MeanI over sigI obs: 2.4 / Rsym value: 0.206 / Redundancy: 1.3 % / Percent possible all: 48.3
Reflection
*PLUS
Rmerge I obs: 0.117
Reflection shell
*PLUS
Percent possible obs: 48.3 / Rmerge I obs: 0.206

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Processing

Software
NameVersionClassification
SADIEdata collection
SAINTdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
SADIEdata reduction
SAINTdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKN
Details: AT FINAL STEP, A RESTRAINED TEMPERATURE FACTOR REFINEMENT WAS CARRIED OUT BY TNT.
R Free selection details: RANDOM / Sigma F: 1.5
Displacement parametersB iso mean: 43.7 Å2 / Aniso B11: 4.6379 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -9.2577 Å2 / Aniso B23: 0 Å2 / Aniso B33: 4.6198 Å2
Least-squares processR factor R free: 0.275 / R factor R work: 0.211 / R factor obs: 0.211 / Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Number reflection R free: 3117 / Number reflection obs: 31019 / Percent reflection R free: 8 / Percent reflection obs: 79.5
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 8330 / Nucleic acid: 0 / Ligand: 168 / Solvent: 0 / Total: 8498
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.326
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
Refine LS restraints ncsNcs model details: RESTRAINTS
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2NAG.PARNAG.TOP
X-RAY DIFFRACTION3TCH.PARTCH.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.326

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