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- PDB-6or3: Structure of an Acyl Intermediate of Thermomyces Lanuginosa Lipas... -

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Basic information

Entry
Database: PDB / ID: 6or3
TitleStructure of an Acyl Intermediate of Thermomyces Lanuginosa Lipase With Palmitic Acid in an Orthorhombic Crystal
ComponentsLipase
KeywordsHYDROLASE / product complex / acyl intermediate / dimer / palmitic acid / LIPID BINDING PROTEIN
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / : / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMcPherson, A.
CitationJournal: Current Enzyme Inhibition / Year: 2020
Title: The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants
Authors: McPherson, A. / Larson, S.B. / Kalasky, A.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 9, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3544
Polymers31,8361
Non-polymers5183
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipase
hetero molecules

A: Lipase
hetero molecules

A: Lipase
hetero molecules

A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,41716
Polymers127,3464
Non-polymers2,07112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
Buried area10450 Å2
ΔGint-64 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.865, 85.268, 86.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 31836.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.17 Å3/Da / Density % sol: 40 % / Description: orthorhombic prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Using filtered culture media with active fungal cells as the stock protein solution, about 30 mg/ml. Sitting drop equal amounts of the protein stock and the reservoir which was 20% PEG 335 ...Details: Using filtered culture media with active fungal cells as the stock protein solution, about 30 mg/ml. Sitting drop equal amounts of the protein stock and the reservoir which was 20% PEG 335 buffered with 0.10 M MES at pH 6.5
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.45→60.8 Å / Num. obs: 46198 / % possible obs: 99.9 % / Redundancy: 62.8 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.334 / Rrim(I) all: 0.337 / Rsym value: 0.32 / Net I/av σ(I): 10.4 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 38.7 % / Rmerge(I) obs: 3.6 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2213 / CC1/2: 0.294 / Rrim(I) all: 3.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TIB

1tib


Resolution: 1.45→60 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.25 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21143 2291 5 %RANDOM
Rwork0.16111 ---
obs0.16355 43893 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.572 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2--1.92 Å20 Å2
3----5.02 Å2
Refinement stepCycle: 1 / Resolution: 1.45→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 32 173 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9463029
X-RAY DIFFRACTIONr_angle_other_deg1.50134680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28123.784111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37115328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3791517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022598
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0443.1561095
X-RAY DIFFRACTIONr_mcbond_other5.0313.1541094
X-RAY DIFFRACTIONr_mcangle_it5.74.7371372
X-RAY DIFFRACTIONr_mcangle_other5.7014.7381373
X-RAY DIFFRACTIONr_scbond_it7.1673.6281122
X-RAY DIFFRACTIONr_scbond_other7.1683.6311123
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5995.2981646
X-RAY DIFFRACTIONr_long_range_B_refined7.03962.84910179
X-RAY DIFFRACTIONr_long_range_B_other7.03862.84710180
X-RAY DIFFRACTIONr_rigid_bond_restr6.70334248
X-RAY DIFFRACTIONr_sphericity_free54.524554
X-RAY DIFFRACTIONr_sphericity_bonded25.70654313
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 196 -
Rwork0.349 3164 -
obs--99.2 %

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