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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 / homology
Function and homology information


retinyl-palmitate esterase activity / acetylesterase / ceramide catabolic process / sterol esterase / sterol ester esterase activity / pancreatic juice secretion / acetylesterase activity / triacylglycerol lipase / triacylglycerol lipase activity / extracellular region / cytoplasm
Similarity search - Function
: / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...: / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TAUROCHOLIC ACID / Bile salt-activated lipase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
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.
History
DepositionJul 30, 1997Processing site: BNL
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 24, 2011Group: Other
Revision 1.4Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.5Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 1.6Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
Polymers118,1312
Non-polymers2,5056
Water00
1
A: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3184
Polymers59,0651
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
Polymers59,0651
Non-polymers1,2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.352585, 0.46694, 0.810957), (0.33472, -0.872206, 0.356677), (0.873868, 0.145684, -0.463821)
Vector: -24.62283, 73.21277, 4.79749)

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Components

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


Mass: 59065.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P30122, sterol esterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H45NO7S
Has protein modificationY

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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 Å3/Da / Density % sol: 61.5 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common 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 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1997
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→17 Å / Num. obs: 33877 / % possible obs: 82.7 % / Observed criterion σ(I): 0.5 / Redundancy: 1.8 % / Biso Wilson estimate: 43.5 Å2 / Rsym value: 0.117 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.206 / % possible all: 48.3
Reflection
*PLUS
Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% 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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKN

1akn


Resolution: 2.8→8 Å / σ(F): 1.5
Details: AT FINAL STEP, A RESTRAINED TEMPERATURE FACTOR REFINEMENT WAS CARRIED OUT BY TNT.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3117 8 %RANDOM
Rwork0.211 ---
obs0.211 31019 79.5 %-
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.6379 Å20 Å20 Å2
2---9.2577 Å20 Å2
3---4.6198 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8330 0 168 0 8498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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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