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- PDB-1isp: Crystal structure of Bacillus subtilis lipase at 1.3A resolution -

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Basic information

Entry
Database: PDB / ID: 1isp
TitleCrystal structure of Bacillus subtilis lipase at 1.3A resolution
Componentslipase
KeywordsHYDROLASE / alpha/beta hydrolase fold
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 / MAD / Resolution: 1.3 Å
AuthorsKawasaki, K. / Kondo, H. / Suzuki, M. / Ohgiya, S. / Tsuda, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution.
Authors: Kawasaki, K. / Kondo, H. / Suzuki, M. / Ohgiya, S. / Tsuda, S.
History
DepositionDec 19, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4752
Polymers19,3831
Non-polymers921
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 58.450, 82.290
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


Mass: 19382.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: pWSL1 / Production host: Bacillus megaterium (bacteria) / Strain (production host): WH320 / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 8000, glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.7-8.8
26-9 %(w/v)PEG80001reservoir
317 %(v/v)glycerol1reservoir
420 mMTris-HCl1droppH7.5
515 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Nov 7, 2000 / Details: BENT PLANE FUSED QUARTZ
RadiationMonochromator: Bent Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 44447 / Num. obs: 44447 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 6.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5209 / % possible all: 79.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 169453
Reflection shell
*PLUS
% possible obs: 79.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1330 2.992 %RANDOM
Rwork0.192 ---
all-44447 --
obs-44447 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 6 151 1508
Refine LS restraintsType: s_bond_d / Dev ideal: 0.029
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.36
LS refinement shell
*PLUS
Rfactor Rwork: 0.265

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