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- PDB-6fz8: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 6fz8
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant L184F/A187F
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: 2.2 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 1.2Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.3Jan 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)44,1493
Polymers44,0431
Non-polymers1052
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 71.870, 114.230
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: 44043.113 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.: 184 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.2→71.87 Å / Num. obs: 21175 / % possible obs: 98.5 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.118 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.316 Å

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Processing

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

4x6u


Resolution: 2.2→57.115 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4
RfactorNum. reflection% reflection
Rfree0.2361 1031 4.88 %
Rwork0.2235 --
obs0.2241 21111 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→57.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 2 184 3302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273208
X-RAY DIFFRACTIONf_angle_d1.8874361
X-RAY DIFFRACTIONf_dihedral_angle_d16.0031135
X-RAY DIFFRACTIONf_chiral_restr0.183450
X-RAY DIFFRACTIONf_plane_restr0.01573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.3160.26071550.27182828X-RAY DIFFRACTION99
2.316-2.46110.32691550.25562826X-RAY DIFFRACTION99
2.4611-2.65110.2551580.23632841X-RAY DIFFRACTION99
2.6511-2.91790.26241290.24312885X-RAY DIFFRACTION99
2.9179-3.34010.21311360.23042859X-RAY DIFFRACTION98
3.3401-4.2080.21751330.2012877X-RAY DIFFRACTION97
4.208-57.13420.20671650.1982964X-RAY DIFFRACTION97

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