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- PDB-2qxt: Crystal Structure Analysis of the Bacillus subtilis lipase crysta... -

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Basic information

Entry
Database: PDB / ID: 2qxt
TitleCrystal Structure Analysis of the Bacillus subtilis lipase crystallized at pH 4.5
ComponentsLipase
KeywordsHYDROLASE / alpha/beta hydrolase fold / Lipid degradation / Secreted
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triglyceride 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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRajakumara, E. / Sankaranarayanan, R.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Structural basis for the remarkable stability of Bacillus subtilis lipase (Lip A) at low pH
Authors: Rajakumara, E. / Acharya, P. / Ahmad, S. / Sankaranaryanan, R. / Rao, N.M.
History
DepositionAug 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water5,044280
1
A: Lipase


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lipase

B: Lipase


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_456y-1,x,-z+11
Buried area990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.936, 74.936, 112.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 19182.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: pET-21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 26% PEG 4000, 50mM Sodium Citrate pH 4.5, 50mM Ammonium Sulfate, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 10, 2003 / Details: mirrors
RadiationMonochromator: Osmic Mirror System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 22197 / Num. obs: 21687 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.106 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2219 / Rsym value: 0.457 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR3451.2.8data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I6W

1i6w


Resolution: 2→24.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2543611.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1093 5 %RANDOM
Rwork0.208 ---
all0.215 22170 --
obs0.208 21661 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.1144 Å2 / ksol: 0.347426 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2--2.26 Å20 Å2
3----4.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 0 280 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.347 94 4.7 %
Rwork0.296 1888 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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