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- PDB-1tgl: A SERINE PROTEASE TRIAD FORMS THE CATALYTIC CENTRE OF A TRIACYLGL... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1tgl
TitleA SERINE PROTEASE TRIAD FORMS THE CATALYTIC CENTRE OF A TRIACYLGLYCEROL LIPASE
ComponentsTRIACYL-GLYCEROL ACYLHYDROLASE
KeywordsHYDROLASE / CARBOXYLIC ESTERASE
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / 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 speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBrady, L. / Brzozowski, A.M. / Derewenda, Z.S. / Dodson, E.J. / Dodson, G.G. / Tolley, S.P. / Turkenburg, J.P. / Christiansen, L. / Huge-Jensen, B. / Norskov, L. / Thim, L.
Citation
Journal: Nature / Year: 1990
Title: A serine protease triad forms the catalytic centre of a triacylglycerol lipase.
Authors: Brady, L. / Brzozowski, A.M. / Derewenda, Z.S. / Dodson, E. / Dodson, G. / Tolley, S. / Turkenburg, J.P. / Christiansen, L. / Huge-Jensen, B. / Norskov, L. / Thim, L. / Menge, U.
#1: Journal: Lipids / Year: 1988
Title: Rhizomucor Miehei Triglyceride Lipase is Synthesized as a Precursor
Authors: Boel, E. / Huge-Jensen, B. / Christensen, M. / Thim, L. / Fiil, N.P.
History
DepositionFeb 5, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIACYL-GLYCEROL ACYLHYDROLASE


Theoretical massNumber of molelcules
Total (without water)29,5091
Polymers29,5091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.600, 75.000, 55.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 34, PRO 209, PRO 229, AND PRO 250 ARE CIS PROLINES.

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Components

#1: Protein TRIACYL-GLYCEROL ACYLHYDROLASE


Mass: 29508.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / References: UniProt: P19515, triacylglycerol lipase
Sequence detailsRESIDUE 156 IN THIS ENTRY IS ASP AS IDENTIFIED BY ELECTRON DENSITY. IN THE PAPER CITED AS REFERENCE ...RESIDUE 156 IN THIS ENTRY IS ASP AS IDENTIFIED BY ELECTRON DENSITY. IN THE PAPER CITED AS REFERENCE 2 ABOVE IT WAS INCORRECTLY ASSIGNED AS GLY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal grow
*PLUS
pH: 8.05 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
215-16 mg/mlprotein1drop
355-75 %(v/v)satphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 21165 / % possible obs: 87.8 % / Rmerge(I) obs: 0.081

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→7.5 Å / Rfactor obs: 0.138
Refinement stepCycle: LAST / Resolution: 1.9→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 0 0 0 286
Refinement
*PLUS
Num. reflection obs: 19305 / Highest resolution: 1.9 Å / Lowest resolution: 7.5 Å / Rfactor all: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.029
X-RAY DIFFRACTIONp_plane_restr0.027

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