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- PDB-1lbt: LIPASE (E.C.3.1.1.3) (TRIACYLGLYCEROL HYDROLASE) -

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Basic information

Entry
Database: PDB / ID: 1lbt
TitleLIPASE (E.C.3.1.1.3) (TRIACYLGLYCEROL HYDROLASE)
ComponentsLIPASE B
KeywordsHYDROLASE (CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYLPENTA(OXYETHYL) HEPTADECANOATE / Lipase B
Similarity search - Component
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsUppenberg, J. / Jones, T.A.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecificity pocket for secondary alcohols.
Authors: Uppenberg, J. / Ohrner, N. / Norin, M. / Hult, K. / Kleywegt, G.J. / Patkar, S. / Waagen, V. / Anthonsen, T. / Jones, T.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Studies of Lipase B from Candida Antarctica
Authors: Uppenberg, J. / Patkar, S. / Bergfors, T. / Jones, T.A.
#2: Journal: Structure / Year: 1994
Title: The Sequence, Crystal Structure Determination and Refinement of Two Crystal Forms of Lipase B from Candida Antarctica
Authors: Uppenberg, J. / Hansen, M.T. / Patkar, S. / Jones, T.A.
History
DepositionJul 11, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / _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 2.1Oct 30, 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 B
B: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9676
Polymers66,0802
Non-polymers1,8864
Water2,792155
1
A: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9833
Polymers33,0401
Non-polymers9432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9833
Polymers33,0401
Non-polymers9432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.100, 50.200, 99.500
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 70 / 2: CIS PROLINE - PRO 192
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0332, 0.0075, -0.9994), (-0.0057, -1, -0.0073), (-0.9994, 0.0055, 0.0332)
Vector: 46.8633, 48.289, 49.5802)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 317 ? 1 .. ? 317

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Components

#1: Protein LIPASE B / TRIACYLGLYCEROL HYDROLASE


Mass: 33040.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida antarctica (fungus) / References: UniProt: P41365, 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.: 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: Chemical ChemComp-T80 / METHYLPENTA(OXYETHYL) HEPTADECANOATE


Mass: 518.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H58O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal grow
*PLUS
Temperature: 20-25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium sulfate1reservoir
210 %dioxane1reservoir
30.1 Msodium citrate1reservoir
410 mg/mlprotein1drop
54 %(w/v)beta-octylglucoside1drop
61.0 1.0ammonium sulfate1drop
710 %dioxane1drop
80.1 Msodium citrate1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE MARK III / Detector: AREA DETECTOR / Date: Jun 18, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26677 / % possible obs: 83 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.041
Reflection
*PLUS
% possible obs: 82 % / Observed criterion σ(I): 0 / Num. measured all: 45529 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 63 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
MARKIIIdata collection
SDMSdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MARKIIIdata reduction
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→7.5 Å / σ(F): 2
RfactorNum. reflection
Rfree0.193 -
Rwork0.172 -
obs0.172 25854
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 128 155 4931
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å

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