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- PDB-1i6w: THE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LIPASE: A MINIMAL ALPH... -

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Basic information

Entry
Database: PDB / ID: 1i6w
TitleTHE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LIPASE: A MINIMAL ALPHA/BETA HYDROLASE ENZYME
ComponentsLIPASE A
KeywordsHYDROLASE / alpha/beta hydrolase
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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
Authorsvan Pouderoyen, G. / Eggert, T. / Jaeger, K.-E. / Dijkstra, B.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of Bacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme.
Authors: van Pouderoyen, G. / Eggert, T. / Jaeger, K.E. / Dijkstra, B.W.
History
DepositionMar 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE A
B: LIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8783
Polymers38,7662
Non-polymers1121
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.639, 83.201, 95.752
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 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 / Plasmid: PMA5LIP / Production host: Bacillus subtilis (bacteria) / Strain (production host): BCL1051 / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: PEG 4000, ethanol amine, sodium sulphate, cadmium chloride, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
22-6 mMglycine1drop
33 mM1reservoirCdCl2
435 %PEG40001reservoir
50.1 Metanol amine1reservoir
620 mM1reservoirNa2S2O4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 1999 / Details: mirrors
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 41851 / Num. obs: 689356 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 13.39 Å2 / Rsym value: 7.6 / Net I/σ(I): 20.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 765 / Rsym value: 28 / % possible all: 30.6
Reflection
*PLUS
Num. obs: 41851 / Num. measured all: 689356 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 30.6 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
DMmodel building
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
DMphasing
RefinementMethod to determine structure: MIR
Starting model: none

Resolution: 1.5→40 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS_TOPPAR:protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2099 5 %5%
Rwork0.181 ---
all0.177 41796 --
obs0.177 41796 81 %-
Solvent computationSolvent model: CNS ANISOTROPIC
Displacement parametersBiso mean: 15.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 1 517 3229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.5→1.51 Å / Total num. of bins used: 41
RfactorNum. reflection% reflection
Rfree0.3854 5 5 %
Rwork0.3344 116 -
obs-121 -
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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