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- PDB-5tgl: A MODEL FOR INTERFACIAL ACTIVATION IN LIPASES FROM THE STRUCTURE ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5tgl
TitleA MODEL FOR INTERFACIAL ACTIVATION IN LIPASES FROM THE STRUCTURE OF A FUNGAL LIPASE-INHIBITOR COMPLEX
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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
N-HEXYLPHOSPHONATE ETHYL ESTER / Lipase
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBrzozowski, A.M. / Derewenda, U. / Derewenda, Z.S. / Dodson, G.G. / Lawson, D. / Turkenburg, J.P. / Bjorkling, F. / Huge-Jensen, B. / Patkar, S.R. / Thim, L.
Citation
Journal: Nature / Year: 1991
Title: A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex.
Authors: Brzozowski, A.M. / Derewenda, U. / Derewenda, Z.S. / Dodson, G.G. / Lawson, D.M. / Turkenburg, J.P. / Bjorkling, F. / Huge-Jensen, B. / Patkar, S.A. / Thim, L.
#1: 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.J. / Dodson, G. / Tolley, S. / Turkenburg, J.P. / Christiansen, L. / Huge-Jensen, B. / Norskov, L. / Thim, L. / Menge, U.
#2: 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
DepositionOct 30, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7182
Polymers29,5241
Non-polymers1941
Water0
1
A: LIPASE
hetero molecules

A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4364
Polymers59,0482
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_456-x-1,y,-z+3/21
Unit cell
Length a, b, c (Å)48.300, 93.900, 122.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES PRO 34, PRO 209, PRO 229, AND PRO 250 ARE CIS PROLINES.

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Components

#1: Protein LIPASE /


Mass: 29523.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / References: UniProt: P19515, triacylglycerol lipase
#2: Chemical ChemComp-HEE / N-HEXYLPHOSPHONATE ETHYL ESTER


Mass: 194.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19O3P
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 1 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
27-10 %(v/v)PEG6001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 5.44 Å / Num. obs: 5892 / % possible obs: 87.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.18 Å / % possible obs: 27.1 % / Redundancy: 2 % / Num. unique obs: 965 / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.185 / Highest resolution: 3 Å
Details: THERE ARE SOME ERRORS IN THE SEQUENCE DUE TO UNCERTAINTY IN THE ORIENTATION OF SIDE CHAINS. THESE DIFFERENCES ARE MINOR AND IN NO WAY COMPROMISE THE OVERALL QUALITY OF THE STRUCTURE OR THE ...Details: THERE ARE SOME ERRORS IN THE SEQUENCE DUE TO UNCERTAINTY IN THE ORIENTATION OF SIDE CHAINS. THESE DIFFERENCES ARE MINOR AND IN NO WAY COMPROMISE THE OVERALL QUALITY OF THE STRUCTURE OR THE SUITABILITY FOR MODELING OR MOLECULAR REPLACEMENT. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN PIR AND PDB SEQUENCE. PIR ENTRY NAME: A34959 PIR RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 181 ASN 181 GLU 220 SER 220
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 0 11 0 297
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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