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- PDB-4x7b: Crystal Structure of lipase from Geobacillus stearothermophilus T... -

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Basic information

Entry
Database: PDB / ID: 4x7b
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant H86Y/A269T
ComponentsLipase
KeywordsHYDROLASE
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 T6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKanteev, M. / Dror, A. / Gihaz, S. / Fishman, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Ministry of Environmental Protection132-2-2 Israel
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.
Authors: Dror, A. / Kanteev, M. / Kagan, I. / Gihaz, S. / Shahar, A. / Fishman, A.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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)44,0063
Polymers43,9011
Non-polymers1052
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 71.750, 114.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Lipase


Mass: 43900.969 Da / Num. of mol.: 1 / Fragment: UNP residues 34-418 / Mutation: H86Y, A269T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus T6 (bacteria)
Plasmid: pET9a / 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.: 176 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.56 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.4→60.778 Å / Num. all: 16204 / Num. obs: 16204 / % possible obs: 97.8 % / Redundancy: 3 % / Biso Wilson estimate: 22.99 Å2 / Rpim(I) all: 0.052 / Rrim(I) all: 0.092 / Rsym value: 0.075 / Net I/av σ(I): 8.267 / Net I/σ(I): 10 / Num. measured all: 48982
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.533.10.1784736623420.1210.1785.199.8
2.53-2.683.10.154.7694222540.1040.156.299.8
2.68-2.8730.1285.4638121260.090.128799.6
2.87-3.12.90.1026.5568219770.0730.1028.799.4
3.1-3.392.80.088.3510617940.0580.0811.598.2
3.39-3.792.90.06410.4462616100.0460.06413.996
3.79-4.382.90.05611.9411814010.0390.05615.594.9
4.38-5.373.10.05312.4365911950.0350.05315.394.7
5.37-7.593.40.05810.732689510.0350.05813.394.3
7.59-34.233.30.04413.218345540.0260.04415.492.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.27 Å
Translation2.5 Å30.27 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.272 Å / FOM work R set: 0.8175 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 811 5.04 %
Rwork0.2041 15267 -
obs0.2063 16078 96.78 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.853 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 84.28 Å2 / Biso mean: 23.5 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.4411 Å2-0 Å20 Å2
2---9.7266 Å2-0 Å2
3---15.1375 Å2
Refinement stepCycle: final / Resolution: 2.4→30.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 2 176 3283
Biso mean--35.15 23.57 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053205
X-RAY DIFFRACTIONf_angle_d0.7234366
X-RAY DIFFRACTIONf_chiral_restr0.051451
X-RAY DIFFRACTIONf_plane_restr0.003570
X-RAY DIFFRACTIONf_dihedral_angle_d11.1091133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.55030.35131290.26692531266099
2.5503-2.74710.31581540.25122526268099
2.7471-3.02330.28231420.23782543268598
3.0233-3.46030.26151380.21212556269498
3.4603-4.35750.19981200.16722513263394
4.3575-30.27450.19061280.17512598272693

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