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

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Basic information

Entry
Database: PDB / ID: 1tic
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 / HYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesRhizopus oryzae (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDerewenda, U. / Swenson, L. / Green, R. / Joerger, R. / Haas, M.J. / 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 1.3Nov 9, 2016Group: Other
Revision 1.4Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPASE
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)59,2472
Polymers59,2472
Non-polymers00
Water00
1
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,6241
Polymers29,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,6241
Polymers29,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.770, 128.860, 78.350
Angle α, β, γ (deg.)90.00, 135.82, 90.00
Int Tables number5
Space group name H-MC1211

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Components

#1: Protein LIPASE / Coordinate model: Cα atoms only


Mass: 29623.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus oryzae (fungus) / References: UniProt: P61872, triacylglycerol lipase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 %protein1drop
240 %ammonium sulfate1reservoir
3100 mMsodium acetate1reservoir
4MPD1reservoir0.020ml
50.05 mMN,N-dimethyl-octadecylamine-N-oxide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 87 % / Rmerge(I) obs: 0.088

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.6→7.5 Å / σ(F): 0 /
RfactorNum. reflection
obs0.16 16876
Refinement stepCycle: LAST / Resolution: 2.6→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 0 0 534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.016
X-RAY DIFFRACTIONp_angle_d0.0560.056
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.1040.104
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6332
X-RAY DIFFRACTIONp_mcangle_it2.5722.5
X-RAY DIFFRACTIONp_scbond_it2.9672.5
X-RAY DIFFRACTIONp_scangle_it4.5584
X-RAY DIFFRACTIONp_plane_restr0.0250.025
X-RAY DIFFRACTIONp_chiral_restr0.0610.061
X-RAY DIFFRACTIONp_singtor_nbd0.1860.186
X-RAY DIFFRACTIONp_multtor_nbd0.2310.231
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1790.179
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.9445
X-RAY DIFFRACTIONp_staggered_tor20.93315
X-RAY DIFFRACTIONp_orthonormal_tor30.9625
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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