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- PDB-7r25: Bacillus pumilus Lipase A -

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Basic information

Entry
Database: PDB / ID: 7r25
TitleBacillus pumilus Lipase A
ComponentsLipase
KeywordsHYDROLASE / lipase / esterase / apo
Function / homologyLipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / Alpha/Beta hydrolase fold / hydrolase activity / CITRIC ACID / PHOSPHATE ION / PROPANOIC ACID / Lipase
Function and homology information
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å
AuthorsLund, B.A.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway262695 Norway
Research Council of Norway274858 Norway
CitationJournal: Biochemistry / Year: 2022
Title: Structure and Mechanism of a Cold-Adapted Bacterial Lipase
Authors: Lund, B.A. / Svalberg, L. / Purg, M. / Chukwu, G. / Widersten, M. / Isaksen, G.V. / Brandsdal, B.O. / Aqvist, J.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)20,8444
Polymers20,4831
Non-polymers3613
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area8430 Å2
Unit cell
Length a, b, c (Å)35.109, 54.697, 40.970
Angle α, β, γ (deg.)90.000, 92.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lipase /


Mass: 20483.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: L5 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) / References: UniProt: W8FKE7
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 18-22 % PEG 4000 0.1-0.5 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.87→35.07 Å / Num. obs: 103387 / % possible obs: 81.78 % / Redundancy: 6.1 % / Biso Wilson estimate: 7.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Net I/σ(I): 30.45
Reflection shellResolution: 0.87→0.9013 Å / Rmerge(I) obs: 0.4447 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1919 / CC1/2: 0.786 / % possible all: 3.1

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
XDS2019data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1isp

1isp


Resolution: 0.87→35.07 Å / SU ML: 0.0492 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.8355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1325 2100 2.03 %
Rwork0.1114 101282 -
obs0.1118 103382 81.78 %
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.66 Å2
Refinement stepCycle: LAST / Resolution: 0.87→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 23 273 1674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851498
X-RAY DIFFRACTIONf_angle_d1.02692034
X-RAY DIFFRACTIONf_chiral_restr0.0864224
X-RAY DIFFRACTIONf_plane_restr0.0106269
X-RAY DIFFRACTIONf_dihedral_angle_d22.0098222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.87-0.890.3362190.2499932X-RAY DIFFRACTION11.29
0.89-0.910.2376480.20642314X-RAY DIFFRACTION28.1
0.91-0.940.2770.17533692X-RAY DIFFRACTION44.98
0.94-0.960.1831080.14435229X-RAY DIFFRACTION63.61
0.96-10.1481520.1297327X-RAY DIFFRACTION88.65
1-1.030.1221700.1128193X-RAY DIFFRACTION99.51
1.03-1.070.12331650.10187988X-RAY DIFFRACTION97.44
1.07-1.120.1051710.0978222X-RAY DIFFRACTION99.67
1.12-1.180.10751690.0998160X-RAY DIFFRACTION99.32
1.18-1.260.12171680.09868084X-RAY DIFFRACTION97.52
1.26-1.350.1321700.10538238X-RAY DIFFRACTION99.88
1.35-1.490.11941680.10828081X-RAY DIFFRACTION98.09
1.49-1.70.12851710.10848254X-RAY DIFFRACTION99.81
1.7-2.150.12111700.11298201X-RAY DIFFRACTION98.82
2.15-35.070.1481740.11468367X-RAY DIFFRACTION99.49

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