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Basic information

Entry
Database: PDB / ID: 6tp8
TitleSubstrate protein interactions in the limbus region of the catalytic site of Candida antarctica Lipase B
ComponentsLipase B
KeywordsHYDROLASE / Lipase / fatty acid/metabolism / lipid chemistry / interfacial enzymology
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
DIETHYL PHOSPHONATE / 2,3-di(butanoyloxy)propyl butanoate / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCianci, M. / Silvestrini, L.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Principles of lipid-enzyme interactions in the limbus region of the catalytic site of Candida antarctica Lipase B.
Authors: Silvestrini, L. / Cianci, M.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
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 / 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_struct_special_symmetry / pdbx_validate_close_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.occupancy / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Jan 24, 2024Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,41311
Polymers99,1213
Non-polymers2,2928
Water26,3201461
1
A: Lipase B
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5087
Polymers66,0802
Non-polymers1,4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-2 kcal/mol
Surface area22190 Å2
MethodPISA
2
C: Lipase B
hetero molecules

C: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8108
Polymers66,0802
Non-polymers1,7306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3620 Å2
ΔGint-0 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.426, 156.654, 138.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-401-

NTK

21C-401-

NTK

31A-900-

HOH

41A-988-

HOH

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Components

#1: Protein Lipase B / CALB


Mass: 33040.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Aspergillus oryzae (mold) / 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.: 3
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-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NTK / 2,3-di(butanoyloxy)propyl butanoate


Mass: 302.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Crystallization trials were performed at 293 K using the hanging-drop method using a Qiagen EasyXtal 15-well plate. A 15 mg.mL CALB solution in 20mM Na(CH3COO) pH = 4.8 was incubated with a ...Details: Crystallization trials were performed at 293 K using the hanging-drop method using a Qiagen EasyXtal 15-well plate. A 15 mg.mL CALB solution in 20mM Na(CH3COO) pH = 4.8 was incubated with a solution of paraoxon-ethyl (SIGMA catalog n. N12816) 30mM in water for one day. 1 uL of CALB solution was diluted with 1 uL of the precipitant solution, made of 200mM Na(CH3COO) pH = 4.8, 20% (w.v) PEG4000, and 15% (v.v) glyceryl tributyrate (SIGMA catalog n. T8626). The drop was equilibrated by vapor diffusion against 500 uL of the precipitant solution. Protein crystals of the CALB complex appeared within two weeks and grew to a size of 0.1 x 0.1 x 0.05 mm3 in five weeks.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.824 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.824 Å / Relative weight: 1
ReflectionResolution: 1.55→67.69 Å / Num. obs: 138806 / % possible obs: 99.18 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 8.4
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1 / Num. unique obs: 48047 / CC1/2: 0.55 / Rpim(I) all: 0.877 / Rrim(I) all: 1.7 / % possible all: 98.05

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.55→67.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.037
RfactorNum. reflection% reflection
Rfree0.1921 7001 5.04 %
Rwork0.163 --
obs0.1644 138777 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.85 Å2
Refinement stepCycle: LAST / Resolution: 1.55→67.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 150 1461 8583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00577388
X-RAY DIFFRACTIONf_angle_d0.904310151
X-RAY DIFFRACTIONf_chiral_restr0.05221191
X-RAY DIFFRACTIONf_plane_restr0.00641324
X-RAY DIFFRACTIONf_dihedral_angle_d5.62475935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.35242190.31784296X-RAY DIFFRACTION97.29
1.57-1.590.2892500.3024317X-RAY DIFFRACTION98.43
1.59-1.610.3072250.27494303X-RAY DIFFRACTION98.46
1.61-1.630.30142320.27114309X-RAY DIFFRACTION98.59
1.63-1.650.2672320.2594341X-RAY DIFFRACTION98.6
1.65-1.670.25762480.24664345X-RAY DIFFRACTION98.65
1.67-1.690.29262260.23764311X-RAY DIFFRACTION98.85
1.69-1.720.26632400.23744344X-RAY DIFFRACTION98.73
1.72-1.750.30552660.24964306X-RAY DIFFRACTION98.98
1.75-1.770.31562470.25214351X-RAY DIFFRACTION98.97
1.77-1.80.25672170.22794389X-RAY DIFFRACTION98.97
1.8-1.840.28111790.20684383X-RAY DIFFRACTION99.09
1.84-1.870.24892220.19294396X-RAY DIFFRACTION99.08
1.87-1.910.21372450.18794331X-RAY DIFFRACTION99.05
1.91-1.950.21392720.1784318X-RAY DIFFRACTION99.35
1.95-20.19952190.16864410X-RAY DIFFRACTION99.27
2-2.050.2182060.16894408X-RAY DIFFRACTION99.33
2.05-2.10.22062550.16774366X-RAY DIFFRACTION99.44
2.1-2.170.19922540.16274383X-RAY DIFFRACTION99.46
2.17-2.240.18972260.15514415X-RAY DIFFRACTION99.42
2.24-2.320.19982520.15474377X-RAY DIFFRACTION99.63
2.32-2.410.2052340.15074387X-RAY DIFFRACTION99.55
2.41-2.520.17512320.14834430X-RAY DIFFRACTION99.57
2.52-2.650.16712070.15264471X-RAY DIFFRACTION99.74
2.65-2.820.19732270.15284453X-RAY DIFFRACTION99.81
2.82-3.030.16642470.15294426X-RAY DIFFRACTION99.83
3.03-3.340.16442350.1494497X-RAY DIFFRACTION99.96
3.34-3.820.15622490.12934471X-RAY DIFFRACTION100
3.82-4.820.13032070.11714563X-RAY DIFFRACTION99.96
4.82-67.690.14682310.14454679X-RAY DIFFRACTION99.47

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