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- PDB-1dte: THE STRUCTURAL ORIGINS OF INTERFACIAL ACTIVATION IN THERMOMYCES (... -

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Basic information

Entry
Database: PDB / ID: 1dte
TitleTHE STRUCTURAL ORIGINS OF INTERFACIAL ACTIVATION IN THERMOMYCES (HUMICOLA) LANUGINOSA LIPASE
ComponentsLIPASE
KeywordsHYDROLASE / lipase / thermomyces linuginosa / interfacial activation / alpa-beta structure
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 / Resolution: 2.35 Å
AuthorsBrozozowski, A.M. / Savage, H.
CitationJournal: Biochemistry / Year: 2000
Title: Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase.
Authors: Brzozowski, A.M. / Savage, H. / Verma, C.S. / Turkenburg, J.P. / Lawson, D.M. / Svendsen, A. / Patkar, S.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: LIPASE
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)58,6852
Polymers58,6852
Non-polymers00
Water5,152286
1
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,3421
Polymers29,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,3421
Polymers29,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.127, 71.096, 82.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein LIPASE


Mass: 29342.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.1
Details: PEG 5000, magnesium chloride, c8e5, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
30.1 MTris-HCl1reservoir
425 mM1reservoirMgCl2
517 %(w/v)mPEG50001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 65466 / Num. obs: 24301 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.116 / Num. unique all: 21108 / % possible all: 49.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 91415 / % possible obs: 98.4 % / Redundancy: 2.75 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 98.6 % / Redundancy: 2.75 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 8.31

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.35→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: data was twinned and detwinned. Thus, probably the reason for higher than normal R-factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.352 1108 -random
Rwork0.263 ---
all-24301 --
obs-21611 88.9 %-
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 0 286 4428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_angle_deg0.048
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.244 / Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_plane_restr0.031

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