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- PDB-1jmy: Truncated Recombinant Human Bile Salt Stimulated Lipase -

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Basic information

Entry
Database: PDB / ID: 1jmy
TitleTruncated Recombinant Human Bile Salt Stimulated Lipase
ComponentsBILE-SALT-ACTIVATED LIPASE
KeywordsHYDROLASE / BSSL / BSDL / Bile salt dependent lipase / Bile salt stimulated lipase
Function / homology
Function and homology information


retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol ester 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 ester esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase / triacylglycerol 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 ...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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMoore, S.A. / Kingston, R.L. / Loomes, K.M. / Hernell, O. / Blackberg, L. / Baker, H.M. / Baker, E.N.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The structure of truncated recombinant human bile salt-stimulated lipase reveals bile salt-independent conformational flexibility at the active-site loop and provides insights into heparin binding.
Authors: Moore, S.A. / Kingston, R.L. / Loomes, K.M. / Hernell, O. / Blackberg, L. / Baker, H.M. / Baker, E.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of native and recombinant human bile-salt dependent lipase: strategies for improvement of diffraction quality
History
DepositionJul 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5752
Polymers57,4791
Non-polymers961
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.640, 90.080, 103.260
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: 57479.176 Da / Num. of mol.: 1 / Fragment: 1-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNUT / Cell line (production host): KIDNEY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19835, triacylglycerol lipase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG-6000, PIPES/KOH, Glycerol, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 3
Details: Kingston, R.L., (2000) Acta Crystallogr., Sect.D, 56, 478.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5-0.8 mg/mlprotein1drop
220 mMMOPS-NH4OH1drop
30.1 M1dropNaCl
40.8 mMCHAPS1drop
50.2 MPIPES-KOH1reservoir
615-25 %PEG60001reservoir
72 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1996 / Details: Graphite Monochromator
RadiationMonochromator: Graphite plus 0.1 mm collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 17429 / Num. obs: 15613 / % possible obs: 89.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.3
Reflection shellHighest resolution: 2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Rsym value: 0.35 / % possible all: 74.9
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 74.9 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Truncated core of acetylcholinesterase

Resolution: 2.6→100 Å / Isotropic thermal model: Tightly restrained individual B's / Cross valid method: Freer / σ(F): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1570 -10% of the reflection set, randomly chosen
Rwork0.236 ---
all-17429 --
obs-15613 89.6 %-
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-11.33 Å20 Å20 Å2
2--16.346 Å20 Å2
3----27.682 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 5 63 4058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.006
X-RAY DIFFRACTIONangles1.6
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.49

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