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- PDB-1trh: TWO CONFORMATIONAL STATES OF CANDIDA RUGOSA LIPASE -

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Basic information

Entry
Database: PDB / ID: 1trh
TitleTWO CONFORMATIONAL STATES OF CANDIDA RUGOSA LIPASE
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / 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
Biological speciesCandida rugosa (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGrochulski, P. / Cygler, M.
Citation
Journal: Protein Sci. / Year: 1994
Title: Two conformational states of Candida rugosa lipase.
Authors: Grochulski, P. / Li, Y. / Schrag, J.D. / Cygler, M.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Insights Into Interfacial Activation from an Open Structure of Candida Rugosa Lipase
Authors: Grochulski, P. / Li, Y. / Schrag, J.D. / Bouthillier, F. / Smith, P. / Harrison, D. / Rubin, B. / Cygler, M.
#2: Journal: Gene / Year: 1993
Title: Cloning and Analysis of Candida Cylindracea Lipase Sequences
Authors: Lotti, M. / Grandori, R. / Fusetti, F. / Longhi, S. / Brocca, S. / Tramontano, A.
#3: Journal: Nature / Year: 1989
Title: The Codon Cug is Read as Serine in an Asporogenic Yeast Candida Cylindracea
Authors: Kawaguchi, Y. / Honda, H. / Taniguchi-Morimura, J. / Iwasaki, S.
History
DepositionNov 18, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 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: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5763
Polymers57,1341
Non-polymers4422
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.000, 106.700, 59.800
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 92 / 2: CIS PROLINE - PRO 390

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Components

#1: Protein LIPASE


Mass: 57133.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida rugosa (fungus) / References: UniProt: P20261, triacylglycerol lipase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: macroseeding / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mLprotein1drop
210 %PEG80001reservoir
3150 mMcacodylate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 30450 / % possible obs: 81 % / Observed criterion σ(I): 1 / Num. measured all: 52852 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.25 Å / % possible obs: 61 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.148 / Rfactor obs: 0.148 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 28 301 4351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.7
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection obs: 20701 / σ(I): 2 / Rfactor all: 0.167 / Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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