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- PDB-1gt6: S146A mutant of Thermomyces (Humicola) lanuginosa lipase complex ... -

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Basic information

Entry
Database: PDB / ID: 1gt6
TitleS146A mutant of Thermomyces (Humicola) lanuginosa lipase complex with oleic acid
ComponentsLipase
KeywordsLIPASE / HYDROLASE / LIPID DEGRADATION / ZYMOGEN
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
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrzozowski, A.M. / Yapoudjian, S. / Ivanova, M.G. / Patkar, S.A. / Vind, J. / Svendsen, A. / Verger, R.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Binding of Thermomyces (Humicola) lanuginosa lipase to the mixed micelles of cis-parinaric acid/NaTDC.
Authors: Yapoudjian, S. / Ivanova, M.G. / Brzozowski, A.M. / Patkar, S.A. / Vind, J. / Svendsen, A. / Verger, R.
History
DepositionJan 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_detector.detector / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2184
Polymers58,6532
Non-polymers5652
Water3,045169
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6092
Polymers29,3261
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6092
Polymers29,3261
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.101, 97.304, 55.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 29326.484 Da / Num. of mol.: 2 / Mutation: S168A
Source method: isolated from a genetically manipulated source
Details: OLEIC ACID / Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Aspergillus oryzae (mold) / References: UniProt: O59952, triacylglycerol lipase
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION SER 168 ALA CHAINS A AND B

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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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.51
Details: PH 8.5 TRIS BUFFER, 25 MM MGCL2, 25% W/V PEG 5K MME, 10 MM PROTEIN CONC 10-20 MG/ML IN 10 MM TRIS BUFFER PH 8.0
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris-HCl11pH8.0
210 mMNaTDC11
325 %(w/v)PEG5000 MME11
425 mM11MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.91 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 33614 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rsym value: 0.075 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.5 / % possible all: 94.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 96.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT5

1dt5


Resolution: 2.2→20 Å / SU B: 5.96346 / SU ML: 0.15322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27451 / ESU R Free: 0.20358
Details: OLEIC ACID IN MOLECULE B IS COMPLETE B IN MOLECULE A ALKYL CHAIN IS VISIBLE TILL C10 CARBON SO THE OCCUPANCY OF THE C11-C18 WERE SET TO 0 (BUT MODELLED).
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 1642 5.1 %RANDOM
Rwork0.21432 ---
obs0.21564 30644 98.1 %-
Displacement parametersBiso mean: 21.158 Å2
Baniso -1Baniso -2Baniso -3
1-5.76 Å20 Å20 Å2
2---3.57 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 40 169 4349
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

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