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- PDB-6fzd: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 6fzd
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 variant L184F/A187F/L360F
ComponentsLipase
KeywordsHYDROLASE / lipase / methanol / organic solvent
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Lipase-like, C-terminal domain / 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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGihaz, S. / Kanteev, M. / Pazy, Y. / Fishman, A.
CitationJournal: Appl.Environ.Microbiol. / Year: 2018
Title: Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol.
Authors: Gihaz, S. / Kanteev, M. / Pazy, Y. / Fishman, A.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: 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)44,1833
Polymers44,0771
Non-polymers1052
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.860, 70.881, 113.167
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


Mass: 44077.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93A71, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→45.63 Å / Num. obs: 37550 / % possible obs: 98.8 % / Redundancy: 7.9 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.051 / Net I/σ(I): 35.3
Reflection shellResolution: 1.8→1.8487 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6U

4x6u


Resolution: 1.8→45.628 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.06
RfactorNum. reflection% reflection
Rfree0.2293 1873 5 %
Rwork0.2118 --
obs0.2126 37486 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 2 271 3392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0283212
X-RAY DIFFRACTIONf_angle_d1.7144366
X-RAY DIFFRACTIONf_dihedral_angle_d15.0571135
X-RAY DIFFRACTIONf_chiral_restr0.287449
X-RAY DIFFRACTIONf_plane_restr0.009574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.28751540.26382719X-RAY DIFFRACTION100
1.8487-1.90310.28911200.23762713X-RAY DIFFRACTION99
1.9031-1.96450.23821440.22452721X-RAY DIFFRACTION99
1.9645-2.03470.29431330.22442689X-RAY DIFFRACTION99
2.0347-2.11620.24871560.21652705X-RAY DIFFRACTION99
2.1162-2.21250.25071470.21652727X-RAY DIFFRACTION99
2.2125-2.32910.22361460.21022695X-RAY DIFFRACTION99
2.3291-2.4750.25261410.21662749X-RAY DIFFRACTION99
2.475-2.66610.23811400.22532656X-RAY DIFFRACTION97
2.6661-2.93440.21391440.22832755X-RAY DIFFRACTION99
2.9344-3.35890.23581450.21172764X-RAY DIFFRACTION99
3.3589-4.23140.20631520.18712792X-RAY DIFFRACTION99
4.2314-45.64240.18841510.19542928X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -10.4492 Å / Origin y: 9.734 Å / Origin z: -18.177 Å
111213212223313233
T0.0893 Å2-0.0161 Å2-0.0036 Å2-0.0928 Å2-0.0051 Å2--0.0894 Å2
L0.5504 °2-0.1577 °20.0149 °2-0.8298 °20.0984 °2--0.4055 °2
S-0.0193 Å °-0.0254 Å °-0.0255 Å °0.0769 Å °-0.0083 Å °-0.0109 Å °0.0264 Å °-0.018 Å °0.0268 Å °
Refinement TLS groupSelection details: all

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