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- PDB-1f6w: STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN BILE SALT ACTIVATED LIPASE -

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Basic information

Entry
Database: PDB / ID: 1f6w
TitleSTRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN BILE SALT ACTIVATED LIPASE
ComponentsBILE SALT ACTIVATED LIPASE
KeywordsHYDROLASE / bile salt activated lipase / esterase / catalytic domain
Function / homology
Function and homology information


retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase ...retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase / triglyceride lipase activity / catalytic activity / lipid metabolic process / heparin binding / hydrolase activity / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Mucin-like domain / Mucin-like / 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 ...Mucin-like domain / Mucin-like / 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
Bile salt-activated lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTerzyan, S. / Zhang, X.
CitationJournal: Protein Sci. / Year: 2000
Title: Crystal structure of the catalytic domain of human bile salt activated lipase.
Authors: Terzyan, S. / Wang, C.S. / Downs, D. / Hunter, B. / Zhang, X.C.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BILE SALT ACTIVATED LIPASE


Theoretical massNumber of molelcules
Total (without water)58,8271
Polymers58,8271
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.7, 88.97, 104.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BILE SALT ACTIVATED LIPASE


Mass: 58826.695 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: A298D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PANCREAS / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19835, triacylglycerol lipase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: PEG 6000, NaCl, N-(2-acetamido) iminodiacetic acid, pH 6.5, EVAPORATION, temperature 293.K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG60001reservoir
2100 mM1reservoirNaCl
3100 mMADA1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 27725 / Num. obs: 25287 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2378 / % possible all: 87.8
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKN

1akn


Resolution: 2.3→24.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 157890557.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk Solvent Model Used
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1171 5 %RANDOM
Rwork0.212 ---
obs0.212 23474 85.6 %-
all-25287 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2893 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---17.67 Å20 Å2
3---20.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 0 163 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it3.122
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 160 4.7 %
Rwork0.36 3232 -
obs--75.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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