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- PDB-6l7n: crystal structure of a FUNGAL LIPASES -

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Basic information

Entry
Database: PDB / ID: 6l7n
Titlecrystal structure of a FUNGAL LIPASES
ComponentsLipase, class 3
KeywordsHYDROLASE / LIPASE
Function / homology
Function and homology information


monocarboxylic acid biosynthetic process / antibiotic biosynthetic process / 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
Similarity search - Domain/homology
Biological speciesPenicillium roqueforti FM164 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, Y.H. / Yuan, H. / Lan, D.M. / Liu, X.H.
CitationJournal: To Be Published
Title: crystal structure of a FUNGAL LIPASES
Authors: Wang, Y.H. / Yuan, H. / Lan, D.M. / Liu, X.H.
History
DepositionNov 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase, class 3


Theoretical massNumber of molelcules
Total (without water)30,8111
Polymers30,8111
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11000 Å2
Unit cell
Length a, b, c (Å)33.247, 44.928, 46.025
Angle α, β, γ (deg.)109.220, 101.360, 112.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Lipase, class 3


Mass: 30811.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium roqueforti FM164 (fungus) / Strain: FM164 / Gene: PROQFM164_S02g000904 / Production host: Pichia kudriavzevii (yeast) / References: UniProt: W6Q990
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 32.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 26% PEG 1500, 0.1 M Sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19035 / % possible obs: 94.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.04 / Net I/σ(I): 23.4
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 12.26 / Num. unique obs: 1069 / Rpim(I) all: 0.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DT3

1dt3


Resolution: 1.8→50 Å / SU ML: 0.2239 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.376
RfactorNum. reflection% reflection
Rfree0.2275 934 5.19 %
Rwork0.1761 --
obs0.1787 18008 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 0 294 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762132
X-RAY DIFFRACTIONf_angle_d0.88812918
X-RAY DIFFRACTIONf_chiral_restr0.0554322
X-RAY DIFFRACTIONf_plane_restr0.0063378
X-RAY DIFFRACTIONf_dihedral_angle_d8.17121658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.890.29251500.19982394X-RAY DIFFRACTION89.17
1.89-2.010.30961130.20412065X-RAY DIFFRACTION75.42
2.01-2.170.23211620.17492540X-RAY DIFFRACTION94.44
2.17-2.390.24121220.18122252X-RAY DIFFRACTION82.43
2.39-2.730.21511160.17962653X-RAY DIFFRACTION96.68
2.73-3.440.2131390.16942661X-RAY DIFFRACTION97.09
3.44-100.19661320.16452509X-RAY DIFFRACTION92.31

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