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- PDB-3tgl: STRUCTURE AND MOLECULAR MODEL REFINEMENT OF RHIZOMUCOR MIEHEI TRI... -

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Basic information

Entry
Database: PDB / ID: 3tgl
TitleSTRUCTURE AND MOLECULAR MODEL REFINEMENT OF RHIZOMUCOR MIEHEI TRIACYLGLYCERIDE LIPASE: A CASE STUDY OF THE USE OF SIMULATED ANNEALING IN PARTIAL MODEL REFINEMENT
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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: Acta Crystallogr.,Sect.B / Year: 1992
Title: STRUCTURE AND MOLECULAR-MODEL REFINEMENT OF RHIZOMUCOR-MIEHEI TRIACYLGLYCERIDE LIPASE - A CASE-STUDY OF THE USE OF SIMULATED ANNEALING IN PARTIAL MODEL REFINEMENT.
Authors: Brzozowski, A.M. / Derewenda, Z.S. / Dodson, E.J. / Dodson, G.G. / Turkenburg, J.P.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: The Crystal and Molecular Structure of the Rhizomucor Miehei Triacylglyceride Lipase at 1.9 Angstroms Resolution
Authors: Derewenda, Z.S. / Derewenda, U. / Dodson, G.G.
#2: 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. / Patka, S.A. / Thim, L.
#3: 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.
History
DepositionJul 29, 1991Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,5941
Polymers29,5941
Non-polymers00
Water4,143230
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: 29594.043 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE 156 IN THIS ENTRY IS ASP AS IDENTIFIED BY ELECTRON DENSITY. IN THE CDNA SEQUENCE IT WAS ...RESIDUE 156 IN THIS ENTRY IS ASP AS IDENTIFIED BY ELECTRON DENSITY. IN THE CDNA SEQUENCE 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal grow
*PLUS
pH: 8.05 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-16 mg/mlprotein1drop
355-75 %(v/v)satphosphate1reservoir
2Tris/HCl1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 3.45 Å / Num. all: 24101 / % possible obs: 82.8 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge F obs: 0.0807

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→7.5 Å / Rfactor obs: 0.129
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 ALA 150 VAL 150 GLY 156 ASP 156
Refinement stepCycle: LAST / Resolution: 1.9→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 0 230 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.01
X-RAY DIFFRACTIONp_angle_d0.0790.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0970.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.231
X-RAY DIFFRACTIONp_mcangle_it5.881.5
X-RAY DIFFRACTIONp_scbond_it9.371.5
X-RAY DIFFRACTIONp_scangle_it11.752
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.2160.1
X-RAY DIFFRACTIONp_singtor_nbd0.210.5
X-RAY DIFFRACTIONp_multtor_nbd0.3030.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor20.4390
X-RAY DIFFRACTIONp_orthonormal_tor33.3890
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 7.5 Å / Num. reflection obs: 18960 / σ(F): 2 / Rfactor obs: 0.129
Solvent computation
*PLUS
Displacement parameters
*PLUS

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