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- PDB-1tia: AN UNUSUAL BURIED POLAR CLUSTER IN A FAMILY OF FUNGAL LIPASES -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1tia
TitleAN UNUSUAL BURIED POLAR CLUSTER IN A FAMILY OF FUNGAL LIPASES
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid catabolic process / hydrolase activity
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
Similarity search - Domain/homology
Mono- and diacylglycerol lipase
Similarity search - Component
Biological speciesPenicillium camemberti (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsDerewenda, U. / Swenson, L. / Yamaguchi, S. / Wei, Y. / Derewenda, Z.S.
Citation
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.
#1: 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 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)30,2061
Polymers30,2061
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)45.570, 47.100, 33.500
Angle α, β, γ (deg.)79.05, 112.14, 70.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LIPASE


Mass: 30205.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium camemberti (fungus) / References: UniProt: P61870, 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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
22 mMDTT1drop
310 %PEG20001reservoir
4100 mMsodium acetate1reservoir
52 mMDTT1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.98 Å / % possible obs: 79.9 % / Redundancy: 1.97 % / Rmerge(I) obs: 0.0511

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→7.5 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 12586
Refinement stepCycle: LAST / Resolution: 2.1→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms292 0 0 0 292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.4132
X-RAY DIFFRACTIONx_mcangle_it2.0522.5
X-RAY DIFFRACTIONx_scbond_it2.5042.5
X-RAY DIFFRACTIONx_scangle_it3.7344
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_d0.030.061
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_planar_d0.030.052
X-RAY DIFFRACTIONx_plane_restr0.0150.017
X-RAY DIFFRACTIONx_chiral_restr0.060.116

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