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- PDB-6s3v: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 6s3v
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant E251C/G332C
ComponentsLipase
KeywordsHYDROLASE / lipase / methanol / organic solvent / disulfide bond
Function / homologytriacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 26, 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

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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)44,0593
Polymers43,9531
Non-polymers1052
Water4,378243
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 area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.160, 71.970, 112.640
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: 43953.121 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) / Variant (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 / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 45.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M sodium citrate, 22% 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: 1.8→56.32 Å / Num. obs: 37629 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.132 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5453 / CC1/2: 0.845 / Rrim(I) all: 0.491 / % possible all: 99.9

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Processing

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

4x6u


Resolution: 2→56.32 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 --0.05
Rwork0.2278 ---
obs-27497 100 %-
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 2→56.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 2 243 3351

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