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- PDB-3g7n: Crystal Structure of a Triacylglycerol Lipase from Penicillium Ex... -

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Basic information

Entry
Database: PDB / ID: 3g7n
TitleCrystal Structure of a Triacylglycerol Lipase from Penicillium Expansum at 1.3
ComponentsLipase
KeywordsHYDROLASE / hydrolase fold
Function / homology
Function and homology information


monocarboxylic acid biosynthetic process / triacylglycerol lipase / triacylglycerol lipase activity / antibiotic biosynthetic process / lipid metabolic process
Similarity search - Function
: / 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
DI(HYDROXYETHYL)ETHER / Triacylglycerol lipase / Lipase
Similarity search - Component
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.3 Å
AuthorsBian, C.B. / Yuan, C. / Chen, L.Q. / Edward, J.M. / Lin, L. / Jiang, L.G. / Huang, Z.X. / Huang, M.D.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of a triacylglycerol lipase from Penicillium expansum at 1.3 A determined by sulfur SAD
Authors: Bian, C.B. / Yuan, C. / Chen, L.Q. / Meehan, E.J. / Jiang, L.G. / Huang, Z.X. / Lin, L. / Huang, M.D.
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88113
Polymers54,6322
Non-polymers1,24911
Water6,449358
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1359
Polymers27,3161
Non-polymers8198
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7464
Polymers27,3161
Non-polymers4303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.270, 88.270, 126.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lipase / Triacylglycerol Lipase


Mass: 27315.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium expansum (fungus) / Gene: PEL / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus)
References: UniProt: Q9HFW6, UniProt: Q7LST4*PLUS, triacylglycerol lipase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsWILD TYPE PROTEIN WAS USED IN THE STUDY. THE SEQUENCE OBTAINED IN THE STRUCTURE IS RELIABLE.

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: AS, PEG400, pH 8.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.9
SYNCHROTRONAPS 22-ID21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMar 26, 2006
MARMOSAIC 300 mm CCD2CCDOct 10, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.91
211
ReflectionRedundancy: 13.4 % / Av σ(I) over netI: 40.13 / Number: 1656937 / Rmerge(I) obs: 0.062 / Χ2: 0.89 / D res high: 1.3 Å / D res low: 50 Å / Num. obs: 123399 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.85099.310.0381.09913
2.222.810010.0520.91113.9
1.942.2210010.0670.9214.1
1.761.9410010.0811.02814.1
1.641.7610010.121.08214.1
1.541.6410010.1620.93913.8
1.461.5410010.2260.83113.7
1.41.4610010.3240.72913.7
1.351.410010.4340.67613.1
1.31.3510010.5160.61510.7
ReflectionResolution: 1.3→50 Å / Num. obs: 123399 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 40.13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.3-1.3510.70.5161,2100
1.35-1.413.10.4341,2100
1.4-1.4613.70.3241,2100
1.46-1.5413.70.2261,2100
1.54-1.6413.80.1621,2100
1.64-1.7614.10.121,2100
1.76-1.9414.10.0811,2100
1.94-2.2214.10.0671,2100
2.22-2.813.90.0521,2100
2.8-50130.0381,299.3

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→39.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.707 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20784 6161 5 %RANDOM
Rwork0.18801 ---
obs0.189 116585 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 76 358 4234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9555409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94924.027149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.031514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0212957
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21898
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22795
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.651.52548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64724096
X-RAY DIFFRACTIONr_scbond_it3.93731433
X-RAY DIFFRACTIONr_scangle_it5.634.51313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 454 -
Rwork0.301 8495 -
obs--100 %

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