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

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Basic information

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


triacylglycerol lipase / triglyceride 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
N-HEXYLPHOSPHONATE ETHYL ESTER / Lipase B
Similarity search - Component
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.6 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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: LIPASE B
D: LIPASE B
E: LIPASE B
F: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,95318
Polymers198,2416
Non-polymers3,71212
Water1,65792
1
A: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: LIPASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6593
Polymers33,0401
Non-polymers6192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.500, 95.600, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 70 / 2: CIS PROLINE - PRO 192
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99935, -0.035999, 0.002023), (-0.035984, -0.99933, -0.006758), (0.002265, 0.006681, -0.999975)-0.1363, 1.7031, 43.2399
2given(-1, 1.0E-6, 2.0E-6), (1.0E-6, 1, 2.0E-6), (-2.0E-6, 2.0E-6, -1)152.9993, 0.0004, 57.8644
3given(-0.99935, 0.035991, -0.002025), (-0.035977, -0.99933, -0.006761), (-0.002267, -0.006684, 0.999975)153.13699, 1.702, 14.625
4given(-0.99935, 0.035998, -0.002024), (-0.035983, -0.99933, -0.00676), (-0.002266, -0.006683, 0.999975)76.6369, 1.7032, -14.308
5given(-1, -1.0E-6, 2.0E-6), (-1.0E-6, 1, 1.0E-6), (-2.0E-6, 1.0E-6, -1)76.5003, 28.9318
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 M2 A 1 .. A 317 ? 1 .. ? 317 M3 A 1 .. A 317 ? 1 .. ? 317 M4 A 1 .. A 317 ? 1 .. ? 317 M5 A 1 .. A 317 ? 1 .. ? 317

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Components

#1: Protein
LIPASE B / TRIACYLGLYCEROL HYDROLASE


Mass: 33040.238 Da / Num. of mol.: 6 / 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.: 6
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-HEE / N-HEXYLPHOSPHONATE ETHYL ESTER


Mass: 194.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H19O3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growDetails: THIS STRUCTURE WAS BUILT USING DATA COLLECTED ON ONE CRYSTAL. THE CRYSTAL SUFFERED FROM MEROHEDRAL TWINNING, WHERE TWO TWIN COMPONENTS CONTRIBUTE TO DIFFERENT DEGREES TO THE DIFFRACTION ...Details: THIS STRUCTURE WAS BUILT USING DATA COLLECTED ON ONE CRYSTAL. THE CRYSTAL SUFFERED FROM MEROHEDRAL TWINNING, WHERE TWO TWIN COMPONENTS CONTRIBUTE TO DIFFERENT DEGREES TO THE DIFFRACTION INTENSITIES. THE DATA SET WAS MODIFIED TO REMOVE THE CONTRIBUTION FROM THE MINOR TWIN COMPONENT, BEFORE THE REFINEMENT. THE MODIFICATION IS CARRIED OUT BY REMOVAL OF SOME REFLECTIONS AND BY INTENSITY CORRECTIONS OF OTHERS. THE DEPOSITED STRUCTURE FACTORS HAVE BEEN MODIFIED.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Mammonium sulfate1reservoir
20.1 Msodium citrate1reservoir
310 %dioxane1reservoir
47.1 mg/mlprotein1drop
50.57 %beta-octylglucoside1drop
60.19 Mammonium sulfate1drop
70.014 Msodium citrate1drop
81.4 %dioxane1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 20, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26271 / % possible obs: 83 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Observed criterion σ(I): 0 / Num. measured all: 55714 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / % possible obs: 55 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
MADNESdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.6→7.5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.255 --
Rwork0.193 --
obs0.193 15621 82.5 %
Displacement parametersBiso mean: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 234 92 14270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
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_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å

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