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- PDB-5ap9: Controlled lid-opening in Thermomyces lanuginosus lipase - a swit... -

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Basic information

Entry
Database: PDB / ID: 5ap9
TitleControlled lid-opening in Thermomyces lanuginosus lipase - a switch for activity and binding
ComponentsLIPASE
KeywordsHYDROLASE / THERMOMYCES LANUGINOSUS LIPASE / ENGINEERED DISULFIDE BRIDGE / CONTROLLED BINDING / DUAL SWITCH / CONTROLLED ACTIVITY
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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
DI(HYDROXYETHYL)ETHER / Lipase
Similarity search - Component
Biological speciesTHERMOMYCES LANUGINOSUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSkjold-Joergensen, J. / Vind, J. / Moroz, O.V. / Blagova, E.V. / Bhatia, V.K. / Svendsen, A. / Wilson, K.S. / Bjerrum, M.J.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Controlled lid-opening in Thermomyces lanuginosus lipase- An engineered switch for studying lipase function.
Authors: Skjold-Jrgensen, J. / Vind, J. / Moroz, O.V. / Blagova, E. / Bhatia, V.K. / Svendsen, A. / Wilson, K.S. / Bjerrum, M.J.
History
DepositionSep 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2527
Polymers58,6452
Non-polymers6085
Water4,378243
1
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7424
Polymers29,3221
Non-polymers4193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5113
Polymers29,3221
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.478, 90.478, 160.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein LIPASE / / TRIACYLGLYCEROL LIPASE


Mass: 29322.457 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 23-291 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOMYCES LANUGINOSUS (fungus) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: O59952, triacylglycerol lipase
#2: 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 / N-Acetylglucosamine


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

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Non-polymers , 4 types, 247 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATIONS I86C, I255C

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: 50 % PEG400, 0.2 M LITHIUM SULFATE, 0.1 M NA-ACETATE PH 4.5, SITTING DROP, VAPOUR DIFFUSION

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorDate: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50.02 Å / Num. obs: 59391 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT3

1dt3


Resolution: 1.8→50.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.243 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUBUNIT A IS BETTER ORDERED, THAN SUBUNIT B. DESCRIPTION IN THE PAPER WILL REFER TO SUBUNIT A
RfactorNum. reflection% reflectionSelection details
Rfree0.19693 3061 4.9 %RANDOM
Rwork0.17152 ---
obs0.17272 59391 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 38 243 4342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194263
X-RAY DIFFRACTIONr_bond_other_d0.0080.023799
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9385828
X-RAY DIFFRACTIONr_angle_other_deg1.49738714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3624.049205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32515598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2321526
X-RAY DIFFRACTIONr_chiral_restr0.1060.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025034
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021048
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_it1.1251.8962164
X-RAY DIFFRACTIONr_mcbond_other1.1251.8962163
X-RAY DIFFRACTIONr_mcangle_it1.7692.8392717
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.652.0852098
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 220 -
Rwork0.231 4288 -
obs--98.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5193-0.18191.42031.3971-1.15854.3387-0.21760.27510.3080.0361-0.1011-0.1907-0.32470.5050.31870.1374-0.0346-0.04230.08780.07530.104527.0091-37.83928.3953
22.86090.92990.21061.29430.14541.37820.0748-0.0191-0.1350.1165-0.0405-0.1390.0015-0.0269-0.03430.09670.0163-0.03470.0173-0.00920.02823.2111-2.1499-8.98
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 269
2X-RAY DIFFRACTION2A2 - 300

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