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- PDB-1tib: CONFORMATIONAL LABILITY OF LIPASES OBSERVED IN THE ABSENCE OF AN ... -

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Basic information

Entry
Database: PDB / ID: 1tib
TitleCONFORMATIONAL LABILITY OF LIPASES OBSERVED IN THE ABSENCE OF AN OIL-WATER INTERFACE: CRYSTALLOGRAPHIC STUDIES OF ENZYMES FROM THE FUNGI HUMICOLA LANUGINOSA AND RHIZOPUS DELEMAR
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
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: 1.84 Å
AuthorsDerewenda, U. / Swenson, L. / Wei, Y. / Derewenda, Z.S.
Citation
Journal: J.Lipid Res. / Year: 1994
Title: Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar.
Authors: Derewenda, U. / Swenson, L. / Wei, Y. / Green, R. / Kobos, P.M. / Joerger, R. / Haas, M.J. / Derewenda, Z.S.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: An Unusual Buried Polar Cluster in a Family of Fungal Lipases
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Dodson, G.G. / Yamaguchi, S. / Haas, M.J. / Derewenda, Z.S.
#2: Journal: Protein Eng. / Year: 1994
Title: Current Progress in Crystallographic Studies of New Lipases from Filamentous Fungi
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Yamaguchi, S. / Joerger, R. / Haas, M.J. / Derewenda, Z.S.
History
DepositionDec 6, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,3421
Polymers29,3421
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.165, 51.994, 45.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 207 / 2: CIS PROLINE - PRO 218

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Components

#1: Protein LIPASE


Mass: 29342.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 %protein1drop
24 %PEG60001reservoir
3100 mMsodium acetate1reservoir
41 mM1reservoircan be replaced by NaAuCl2K2PdCl4
53 mMspermidine1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.85 Å / % possible obs: 100 % / Rmerge(I) obs: 0.0472

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.84→7.5 Å / σ(F): 0 /
RfactorNum. reflection
obs0.188 19345
Refinement stepCycle: LAST / Resolution: 1.84→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 0 356 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.015
X-RAY DIFFRACTIONp_angle_d0.0550.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1442
X-RAY DIFFRACTIONp_mcangle_it1.8092.5
X-RAY DIFFRACTIONp_scbond_it2.2072.5
X-RAY DIFFRACTIONp_scangle_it3.9874
X-RAY DIFFRACTIONp_plane_restr0.0180.015
X-RAY DIFFRACTIONp_chiral_restr0.1040.06
X-RAY DIFFRACTIONp_singtor_nbd0.1660.15
X-RAY DIFFRACTIONp_multtor_nbd0.2160.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2030.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.0133
X-RAY DIFFRACTIONp_staggered_tor20.65710
X-RAY DIFFRACTIONp_orthonormal_tor32.01915
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor all: 0.18 / Rfactor obs: 0.167 / Highest resolution: 1.85 Å / Num. reflection obs: 18756 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.9
X-RAY DIFFRACTIONp_plane_restr0.016

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