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- PDB-6s3j: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 6s3j
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 variant E134C/F149C
ComponentsLipase
KeywordsHYDROLASE / lipase / methanol / organic solvent / disulfide bond
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: 1.9 Å
AuthorsGihaz, S. / Bash, Y. / Rush, I. / Shahar, A. / Pazy, Y. / Fishman, A.
CitationJournal: Chemcatchem / Year: 2019
Title: Bridges to Stability: Engineering Disulfide Bonds Towards Enhanced Lipase Biodiesel Synthesis
Authors: Gihaz, S. / Bash, Y. / Rush, I. / Shahar, A. / Pazy, Y. / Fishman, A.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,9683
Polymers43,8631
Non-polymers1052
Water6,179343
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.593, 71.587, 113.861
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: 43863.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): SHuffle / 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.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M sodium citrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→44.56 Å / Num. obs: 32174 / % possible obs: 98.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 18.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.104 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4652 / CC1/2: 0.768 / Rrim(I) all: 0.84 / % possible all: 99

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6U

4x6u


Resolution: 1.9→44.56 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --0.05
Rwork0.2243 ---
obs-32061 98.2 %-
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 2 343 3444

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