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- PDB-3o0d: Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 3o0d
TitleCrystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution
ComponentsTriacylglycerol lipase
KeywordsHYDROLASE / alpha/beta-Hydrolase / lipase / lipids binding / glycosylation / extracellular
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Triacylglycerol lipase
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBordes, F. / Tranier, S. / Mourey, L. / Marty, A.
CitationJournal: Biophys.J. / Year: 2010
Title: Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.
Authors: Bordes, F. / Barbe, S. / Escalier, P. / Mourey, L. / Andre, I. / Marty, A. / Tranier, S.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
D: Triacylglycerol lipase
E: Triacylglycerol lipase
F: Triacylglycerol lipase
G: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,28945
Polymers233,9097
Non-polymers5,38038
Water29,7791653
1
A: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3708
Polymers33,4161
Non-polymers9547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2527
Polymers33,4161
Non-polymers8366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2527
Polymers33,4161
Non-polymers8366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2527
Polymers33,4161
Non-polymers8366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1336
Polymers33,4161
Non-polymers7185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1336
Polymers33,4161
Non-polymers7185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8974
Polymers33,4161
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.354, 132.141, 137.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 21 molecules ABCDEFG

#1: Protein
Triacylglycerol lipase / / YALI0A20350p


Mass: 33415.621 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: lip2, YALI0A20350g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9P8F7, triacylglycerol lipase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1677 molecules

#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1653 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% MPD, 0.1M MES, 0.02M CaCl2, 0.2M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2007
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 229642 / Num. obs: 228540 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 6.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 33221 / Rsym value: 0.343 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.962 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21096 11428 5 %RANDOM
Rwork0.17062 ---
all0.17264 229642 --
obs0.17264 216938 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0 Å2
2--0.73 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16269 0 339 1653 18261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02217431
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.95523882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66852191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62324.951816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74152597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2061554
X-RAY DIFFRACTIONr_chiral_restr0.1690.22666
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02113547
X-RAY DIFFRACTIONr_mcbond_it1.4111.510637
X-RAY DIFFRACTIONr_mcangle_it2.244217301
X-RAY DIFFRACTIONr_scbond_it3.22136794
X-RAY DIFFRACTIONr_scangle_it4.8244.56552
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 805 -
Rwork0.262 15885 -
obs--99.87 %

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