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- PDB-1llf: Cholesterol Esterase (Candida Cylindracea) Crystal Structure at 1... -

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Basic information

Entry
Database: PDB / ID: 1llf
TitleCholesterol Esterase (Candida Cylindracea) Crystal Structure at 1.4A resolution
ComponentsLipase 3
KeywordsHYDROLASE / Candida cylindracea cholesterol esterase / sterol ester acylhydrolase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / cholesterol metabolic process
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
TRICOSANOIC ACID / Lipase 3 / Lipase
Similarity search - Component
Biological speciesCandida cylindracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPletnev, V. / Addlagatta, A. / Wawrzak, Z. / Duax, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 A resolution.
Authors: Pletnev, V. / Addlagatta, A. / Wawrzak, Z. / Duax, W.
#1: Journal: Structure / Year: 1995
Title: Structure of uncomplexed and linoleate-bound Candida cylindracea cholesterol esterase
Authors: Ghosh, D. / Wawrzak, Z. / Pletnev, V.Z. / Li, N. / Kaiser, R. / Pangborn, W. / Jornvall, H. / Erman, M. / Duax, W.L.
History
DepositionApr 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase 3
B: Lipase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0948
Polymers114,6872
Non-polymers2,4076
Water19,4201078
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.461, 58.477, 89.515
Angle α, β, γ (deg.)92.71, 97.48, 109.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lipase 3 / Cholesterol Esterase


Mass: 57343.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida cylindracea (fungus)
References: UniProt: p32947, UniProt: Q6S5M9*PLUS, triacylglycerol lipase
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-F23 / TRICOSANOIC ACID


Mass: 354.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, potassium phosphate, detergent Thesit, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
250 mMphosphate1droppH7.3
321 %PEG1reservoir
1PEG33501drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2001 / Details: focusing mirrors
RadiationMonochromator: double crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 206525 / Num. obs: 206525 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 7.8 / Num. unique all: 35868 / % possible all: 88
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 1424531
Reflection shell
*PLUS
% possible obs: 88 % / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLE

1cle


Resolution: 1.4→30 Å / Isotropic thermal model: anisotropic / Cross valid method: Free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: SHELDRICK
Details: Konnert-Hendrickson conjugate gradient least squares algorithm
RfactorNum. reflection% reflectionSelection details
Rfree0.169 10338 -RANDOM
Rwork0.136 ---
all0.142 196187 --
obs0.142 196187 90.2 %-
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 162 1078 9314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.004
X-RAY DIFFRACTIONs_from_restr_planes0.377
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.106
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.036
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.4-1.50.128X-RAY DIFFRACTION3586888.04
1.5-1.670.116X-RAY DIFFRACTION4321088.84
1.67-1.920.116X-RAY DIFFRACTION3897989.18
1.92-2.50.118X-RAY DIFFRACTION4230091.67
2.5-300.161X-RAY DIFFRACTION3583193.85
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.03
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg24.44
X-RAY DIFFRACTIONs_plane_restr0.377
X-RAY DIFFRACTIONs_chiral_restr0.063

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