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- PDB-1lgy: LIPASE II FROM RHIZOPUS NIVEUS -

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Basic information

Entry
Database: PDB / ID: 1lgy
TitleLIPASE II FROM RHIZOPUS NIVEUS
ComponentsTRIACYLGLYCEROL LIPASE
KeywordsHYDROLASE (CARBOXYLIC ESTER) / LIPASE
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhizopus niveus (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKohno, M. / Funatsu, J. / Mikami, B. / Kugimiya, W. / Matsuo, T. / Morita, Y.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1996
Title: The crystal structure of lipase II from Rhizopus niveus at 2.2 A resolution.
Authors: Kohno, M. / Funatsu, J. / Mikami, B. / Kugimiya, W. / Matsuo, T. / Morita, Y.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 1994
Title: Purification, Characterization and Crystallization of Two Types of Lipase from Rhizopus Niveus
Authors: Kohno, M. / Kugimiya, W. / Hashimoto, Y. / Morita, Y.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Investigation of Crystals of Lipase I from Rhizopus Niveus
Authors: Kohno, M. / Kugimiya, W. / Hashimoto, Y. / Morita, Y.
History
DepositionMay 23, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIACYLGLYCEROL LIPASE
B: TRIACYLGLYCEROL LIPASE
C: TRIACYLGLYCEROL LIPASE


Theoretical massNumber of molelcules
Total (without water)88,8713
Polymers88,8713
Non-polymers00
Water8,611478
1
A: TRIACYLGLYCEROL LIPASE


Theoretical massNumber of molelcules
Total (without water)29,6241
Polymers29,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRIACYLGLYCEROL LIPASE


Theoretical massNumber of molelcules
Total (without water)29,6241
Polymers29,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRIACYLGLYCEROL LIPASE


Theoretical massNumber of molelcules
Total (without water)29,6241
Polymers29,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.700, 83.700, 137.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999623, 0.025854, -0.009201), (-0.026266, -0.998509, 0.047852), (-0.007951, 0.048076, 0.998812)123.0281, 124.3696, -2.0961
2given(-0.071585, -0.69806, 0.712452), (-0.608659, 0.596448, 0.523244), (-0.790196, -0.396184, -0.467577)77.6261, 54.8681, 140.705

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Components

#1: Protein TRIACYLGLYCEROL LIPASE / LIPASE


Mass: 29623.504 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhizopus niveus (fungus) / References: UniProt: P61871, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 47 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114-18 %PEG80001reservoir
20.1 MHEPES1reservoir
318 mg/mlprotein1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 16, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 53656 / % possible obs: 86.7 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 78 %

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Processing

Software
NameClassification
RIGAKUdata collection
X-PLORmodel building
TNTrefinement
X-PLORrefinement
RIGAKUdata reduction
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: CHARMM MEAN B VALUE 22.6 ANGSTROMS**2 ESD FROM LUZZATI PLOT 0.30 ANGSTROMS X-PLOR ALSO WAS USED.
RfactorNum. reflection
Rwork0.186 -
obs-40601
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 0 0 478 6682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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