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- PDB-4x6u: Crystal Structure of lipase from Geobacillus stearothermophilus T6 -

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Basic information

Entry
Database: PDB / ID: 4x6u
TitleCrystal Structure of lipase from Geobacillus stearothermophilus T6
ComponentsLipase
KeywordsHYDROLASE / esterase
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0383
Polymers43,9331
Non-polymers1052
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.979, 71.570, 113.332
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: 43933.000 Da / Num. of mol.: 1 / Fragment: UNP residues 33-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (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.: 199 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
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: May 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21199 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 28.93 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Χ2: 1.005 / Net I/av σ(I): 19.651 / Net I/σ(I): 9.9 / Num. measured all: 153775
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.70.43210440.9270.1770.4680.863100
2.24-2.2870.40110360.9260.160.4330.882100
2.28-2.327.30.36110340.9490.1420.3880.813100
2.32-2.377.30.34210470.9580.1340.3670.842100
2.37-2.427.40.31110450.960.1210.3340.846100
2.42-2.487.40.30410430.9640.1190.3270.934100
2.48-2.547.60.2710270.9730.1040.290.876100
2.54-2.617.50.24510560.9730.0950.2630.924100
2.61-2.697.60.2310410.9750.0890.2471.036100
2.69-2.777.60.20210500.9830.0770.2160.969100
2.77-2.877.70.18610520.9820.0710.1991.012100
2.87-2.997.60.16310610.9890.0630.1751.073100
2.99-3.127.60.13510580.9890.0520.1451.076100
3.12-3.297.50.11510480.9910.0450.1241.115100
3.29-3.497.40.09410650.9920.0370.1011.117100
3.49-3.767.20.08610710.9930.0350.0931.127100
3.76-4.147.10.07610740.9940.0310.0821.17799.9
4.14-4.746.90.07210880.9930.030.0781.125100
4.74-5.976.90.07410950.9940.0310.081.17299.7
5.97-5060.06411640.9950.0290.0711.09897.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.99 Å
Translation2.5 Å24.99 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→24.989 Å / FOM work R set: 0.8496 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1081 5.12 %
Rwork0.1908 20040 -
obs0.1928 21121 99.36 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.334 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 79.73 Å2 / Biso mean: 29.49 Å2 / Biso min: 15.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.5488 Å20 Å20 Å2
2--1.1354 Å2-0 Å2
3---0.7194 Å2
Refinement stepCycle: final / Resolution: 2.201→24.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 2 199 3308
Biso mean--37.07 33.17 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113207
X-RAY DIFFRACTIONf_angle_d1.0954362
X-RAY DIFFRACTIONf_chiral_restr0.075452
X-RAY DIFFRACTIONf_plane_restr0.005571
X-RAY DIFFRACTIONf_dihedral_angle_d13.051134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2015-2.30160.27811200.19072381250196
2.3016-2.42290.25391300.18124722602100
2.4229-2.57450.2821400.190324772617100
2.5745-2.7730.25381400.196924842624100
2.773-3.05170.2561520.204324732625100
3.0517-3.49220.25561350.195625212656100
3.4922-4.39590.18561460.178925432689100
4.3959-24.99110.20041180.193426892807100

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