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- PDB-6a12: X-ray structure of lipase from Geobacillus thermoleovorans -

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Basic information

Entry
Database: PDB / ID: 6a12
TitleX-ray structure of lipase from Geobacillus thermoleovorans
ComponentsLipase
KeywordsHYDROLASE / Lipase / Geobacillus thermoleovorans
Function / homologytriacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase
Function and homology information
Biological speciesGeobacillus thermoleovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsMoharana, T.R. / Pal, B. / Rao, N.M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: X-ray structure and characterization of a thermostable lipase from Geobacillus thermoleovorans.
Authors: Moharana, T.R. / Pal, B. / Rao, N.M.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4343
Polymers43,3281
Non-polymers1052
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.140, 72.291, 112.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipase / Thermostable lipase


Mass: 43328.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoleovorans (bacteria) / Gene: lipA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8L1V2, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 386 LEU and 387 ARG are from variant of Geobacillus thermoleovorans.

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 0.1M Sodium cacodylate buffer, pH 6.83, 0.4M magnesium acetate, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 22506 / % possible obs: 97.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.7
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.297 / Num. unique obs: 509 / % possible all: 47

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KU0

1ku0


Resolution: 2.145→45.025 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.2209 1100 4.9 %
Rwork0.1726 --
obs0.1749 22456 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.145→45.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 2 116 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083127
X-RAY DIFFRACTIONf_angle_d1.0064252
X-RAY DIFFRACTIONf_dihedral_angle_d13.1311112
X-RAY DIFFRACTIONf_chiral_restr0.041443
X-RAY DIFFRACTIONf_plane_restr0.005559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1445-2.24210.26671370.19522494X-RAY DIFFRACTION94
2.2421-2.36030.26121290.18212614X-RAY DIFFRACTION99
2.3603-2.50820.24011410.19072650X-RAY DIFFRACTION100
2.5082-2.70180.23041320.18892652X-RAY DIFFRACTION100
2.7018-2.97370.2271450.19582666X-RAY DIFFRACTION100
2.9737-3.40380.23561430.1852691X-RAY DIFFRACTION100
3.4038-4.28790.18511450.14732710X-RAY DIFFRACTION100
4.2879-45.03530.19831280.14922879X-RAY DIFFRACTION100

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