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- PDB-2bce: CHOLESTEROL ESTERASE FROM BOS TAURUS -

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Basic information

Entry
Database: PDB / ID: 2bce
TitleCHOLESTEROL ESTERASE FROM BOS TAURUS
ComponentsCHOLESTEROL ESTERASE
KeywordsHYDROLASE / SERINE ESTERASE / LIPASE
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 ...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 / membrane / cytoplasm
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, J.C.-H. / Miercke, L.J.W. / Krucinski, J. / Starr, J.R. / Saenz, G. / Wang, X. / Spilburg, C.A. / Lange, L.G. / Ellsworth, J.L. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 1998
Title: Structure of bovine pancreatic cholesterol esterase at 1.6 A: novel structural features involved in lipase activation.
Authors: Chen, J.C. / Miercke, L.J. / Krucinski, J. / Starr, J.R. / Saenz, G. / Wang, X. / Spilburg, C.A. / Lange, L.G. / Ellsworth, J.L. / Stroud, R.M.
History
DepositionJan 28, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 23, 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

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Assembly

Deposited unit
A: CHOLESTEROL ESTERASE


Theoretical massNumber of molelcules
Total (without water)63,6251
Polymers63,6251
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.420, 54.250, 106.340
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CHOLESTEROL ESTERASE / BILE SALT ACTIVATED LIPASE / BILE SALT STIMULATED LIPASE


Mass: 63625.395 Da / Num. of mol.: 1 / Mutation: N187Q, N361Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS
Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK)
Production host: Homo sapiens (human) / References: UniProt: P30122, sterol esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-6 mg/mlprotein1drop
22 mMsodium phosphate1drop
30.1 Msodium acetate1reservoir
41.5 Mammonium sulfate1reservoir
56 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 66076 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 8.76 Å2 / Rsym value: 0.087 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.63 Å / % possible all: 68.1
Reflection
*PLUS
Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 68.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 1.6→40 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2768 7 %RANDOM
Rwork0.211 ---
obs0.211 41183 89.1 %-
Displacement parametersBiso mean: 14.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.254 Å0.21 Å
Luzzati d res low-40 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 0 0 199 731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.377
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2964 117 7 %
Rwork0.2831 1644 -
obs--68.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.2831

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