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- PDB-1gz7: Crystal structure of the closed state of lipase 2 from Candida rugosa -

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Basic information

Entry
Database: PDB / ID: 1gz7
TitleCrystal structure of the closed state of lipase 2 from Candida rugosa
ComponentsLIPASE 2
KeywordsHYDROLASE / CARBOXYLIC ESTERASE / GLYCOPROTEIN.
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMancheno, J.M. / Hermoso, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structural Insights Into the Lipase/Esterase Behavior in the Candida Rugosa Lipases Family: Crystal Structure of the Lipase 2 Isoenzyme at 1.97A Resolution
Authors: Mancheno, J.M. / Pernas, M.A. / Martinez, M.J. / Ochoa, B. / Rua, M.L. / Hermoso, J.A.
#1: Journal: Methods Enzymol. / Year: 1997
Title: Cloning, Sequencing, and Expression of Candida Rugosa Lipases
Authors: Alberghina, L. / Lotti, M.
#2: 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
DepositionMay 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_chiral / pdbx_validate_symm_contact / 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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 2.1Dec 13, 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
Revision 2.2Nov 13, 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: LIPASE 2
B: LIPASE 2
C: LIPASE 2
D: LIPASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,47216
Polymers230,0374
Non-polymers2,43412
Water26,5001471
1
A: LIPASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1184
Polymers57,5091
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1184
Polymers57,5091
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LIPASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1184
Polymers57,5091
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LIPASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1184
Polymers57,5091
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 91.140, 108.460
Angle α, β, γ (deg.)90.78, 106.31, 86.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
LIPASE 2


Mass: 57509.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) CANDIDA RUGOSA (fungus) / References: UniProt: P32946, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1471 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.5 / Details: 15% (W/V) PEG 4000, SODIUM ACETATE 0.1M, PH 5.0
Crystal grow
*PLUS
Temperature: 291 K / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG40001reservoir
20.1 Msodium acetate1reservoirpH5.0
37-8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004
DetectorDetector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 1.97→37.11 Å / Num. obs: 152503 / % possible obs: 94.6 % / Redundancy: 2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.6
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / % possible all: 76.5
Reflection
*PLUS
Highest resolution: 1.97 Å / Num. measured all: 299637 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 76.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRH

1trh


Resolution: 1.97→11.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 935285.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY CORRESPONDING TO RESIDUES 78 AND 79 IS NOT CONSISTENT WITH THE SEQUENCE DESCRIBED FOR LIPASE2 (ARG-HIS), BUT WITH LEU-ASP, PRECISELY THE SEQUENCE DESCRIBED FOR LIPASE 1 AND LIPASE 3.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 7672 5.1 %RANDOM
Rwork0.2 ---
obs0.2 151824 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0866 Å2 / ksol: 0.42525 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å28.08 Å2-8.09 Å2
2---2.09 Å20.57 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.97→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16212 0 160 1471 17843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 1074 5.1 %
Rwork0.315 19977 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCRY_XPLOR_TOP.TXT
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4CRY_XPLOR_PAR.TXT
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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