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- PDB-1cle: STRUCTURE OF UNCOMPLEXED AND LINOLEATE-BOUND CANDIDA CYLINDRACEA ... -

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Basic information

Entry
Database: PDB / ID: 1cle
TitleSTRUCTURE OF UNCOMPLEXED AND LINOLEATE-BOUND CANDIDA CYLINDRACEA CHOLESTEROL ESTERASE
ComponentsCHOLESTEROL ESTERASE
KeywordsLIPASE / ESTERASE / SUBSTRATE/PRODUCT-BOUND
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / cholesterol metabolic process / lipid catabolic process
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
CHOLESTERYL LINOLEATE / PHOSPHATE ION / Lipase 3
Similarity search - Component
Biological speciesCandida cylindracea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsGhosh, D.
Citation
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.
#1: Journal: FEBS Lett. / Year: 1994
Title: Monomeric and Dimeric Forms of Cholesterol Esterase from Candida Cylindracea: Primary Structure, Identity in Peptide Patterns, and Additional Microheterogeneity
Authors: Kaiser, R. / Erman, M. / Duax, W.L. / Ghosh, D. / Jornvall, H.
#2: Journal: J.Steroid Biochem.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary Diffraction Analysis of Cholesterol Esterase from Candida Cylindracea
Authors: Ghosh, D. / Erman, M. / Duax, W.L.
History
DepositionFeb 8, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: CHOLESTEROL ESTERASE
B: CHOLESTEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,43810
Polymers114,6592
Non-polymers2,7798
Water8,611478
1
A: CHOLESTEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7195
Polymers57,3291
Non-polymers1,3904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHOLESTEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7195
Polymers57,3291
Non-polymers1,3904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.790, 90.920, 58.790
Angle α, β, γ (deg.)93.39, 105.74, 97.22
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 390 / 2: CIS PROLINE - PRO B 390

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CHOLESTEROL ESTERASE


Mass: 57329.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida cylindracea (fungus) / References: UniProt: P32947

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Sugars , 2 types, 4 molecules

#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.: 2
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: 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

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Non-polymers , 3 types, 482 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CLL / CHOLESTERYL LINOLEATE


Mass: 649.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H76O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: please refer to McPherson, A., Preparation and Analysis of Protein Crystals. Wiley, New York (1982)

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 119382 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 62706 / Num. measured all: 119382 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
RIGAKUdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
RIGAKUdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.149 -
obs0.149 54351
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8072 0 188 478 8738
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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