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- PDB-5cri: Wild-type Bacillus subtilis lipase A with 0% [BMIM][Cl] -

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Basic information

Entry
Database: PDB / ID: 5cri
TitleWild-type Bacillus subtilis lipase A with 0% [BMIM][Cl]
ComponentsEsterase
KeywordsHYDROLASE / wild-type
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipase / Lipase EstA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.63 Å
AuthorsNordwald, E.M. / Plaks, J.G. / Snell, J.R. / Sousa, M.C. / Kaar, J.L.
CitationJournal: Chembiochem / Year: 2015
Title: Crystallographic Investigation of Imidazolium Ionic Liquid Effects on Enzyme Structure.
Authors: Nordwald, E.M. / Plaks, J.G. / Snell, J.R. / Sousa, M.C. / Kaar, J.L.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2467
Polymers38,7662
Non-polymers4805
Water8,539474
1
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7675
Polymers19,3831
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4792
Polymers19,3831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.254, 82.622, 95.150
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 Esterase / Lipase / Lipase A


Mass: 19382.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA, QX56_01625 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: I6V559, UniProt: P37957*PLUS, triacylglycerol lipase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 35 % PEG 3350, 0.1M ethanolamine, 20 mM NaSO4, 10 mM ZnCl2
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→30.3 Å / Num. obs: 39315 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.2
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
RefinementResolution: 1.63→24.421 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1638 1970 5.12 %
Rwork0.1278 --
obs0.1296 38497 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→24.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 25 474 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012770
X-RAY DIFFRACTIONf_angle_d1.2743754
X-RAY DIFFRACTIONf_dihedral_angle_d12.805976
X-RAY DIFFRACTIONf_chiral_restr0.074416
X-RAY DIFFRACTIONf_plane_restr0.006482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6302-1.6710.21221330.12752389X-RAY DIFFRACTION92
1.671-1.71620.18881340.11152516X-RAY DIFFRACTION95
1.7162-1.76670.19781340.11192524X-RAY DIFFRACTION96
1.7667-1.82370.19241350.12762495X-RAY DIFFRACTION96
1.8237-1.88880.19271380.12472573X-RAY DIFFRACTION97
1.8888-1.96440.18511410.12172609X-RAY DIFFRACTION98
1.9644-2.05380.16631410.11592590X-RAY DIFFRACTION99
2.0538-2.1620.1671430.11372639X-RAY DIFFRACTION99
2.162-2.29740.14711420.11692645X-RAY DIFFRACTION99
2.2974-2.47460.14361420.11442653X-RAY DIFFRACTION100
2.4746-2.72330.15871420.12442638X-RAY DIFFRACTION99
2.7233-3.11670.16091450.13432690X-RAY DIFFRACTION99
3.1167-3.92410.16771470.13092743X-RAY DIFFRACTION100
3.9241-24.42380.14681530.14962823X-RAY DIFFRACTION99

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