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- PDB-7e04: Crystal structure of Bomgl, a monoacylglycerol lipase from marine... -

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Basic information

Entry
Database: PDB / ID: 70000
TitleCrystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus sp.
ComponentsLipase
KeywordsHYDROLASE / Lipase / monoacylglycerol / marine bacterial
Function / homologyEsterase/lipase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Lipase
Function and homology information
Biological speciesCytobacillus oceanisediminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsWang, Y.H. / Wang, J. / Lan, D.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725022 China
CitationJournal: To Be Published
Title: Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus
Authors: Wang, Y.H. / Wang, J. / Lan, D.M.
History
DepositionJan 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4482
Polymers28,3561
Non-polymers921
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-2 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.280, 87.280, 117.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-744-

HOH

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Components

#1: Protein Lipase


Mass: 28356.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytobacillus oceanisediminis (bacteria)
Gene: BBV17_11975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S1YN08
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.25→27.75 Å / Num. obs: 72862 / % possible obs: 99.7 % / Redundancy: 30.7 % / Biso Wilson estimate: 9.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.5
Reflection shellResolution: 1.25→1.28 Å / Rmerge(I) obs: 0.925 / Num. unique obs: 5134 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xks

5xks


Resolution: 1.25→23.14 Å / SU ML: 0.1208 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.181 3564 4.9 %
Rwork0.1715 69211 -
obs0.1719 72775 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.49 Å2
Refinement stepCycle: LAST / Resolution: 1.25→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 6 352 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491989
X-RAY DIFFRACTIONf_angle_d0.83422698
X-RAY DIFFRACTIONf_chiral_restr0.0778306
X-RAY DIFFRACTIONf_plane_restr0.006344
X-RAY DIFFRACTIONf_dihedral_angle_d5.1776272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.34471310.32682604X-RAY DIFFRACTION95.4
1.27-1.290.32251160.27542694X-RAY DIFFRACTION97.94
1.29-1.30.24681490.24032716X-RAY DIFFRACTION99.44
1.3-1.320.22561480.20842710X-RAY DIFFRACTION100
1.32-1.350.23141500.20122725X-RAY DIFFRACTION100
1.35-1.370.22081400.19682725X-RAY DIFFRACTION100
1.37-1.390.20361250.18952749X-RAY DIFFRACTION100
1.39-1.420.19741450.18832743X-RAY DIFFRACTION100
1.42-1.450.18851250.17172762X-RAY DIFFRACTION100
1.45-1.480.18761630.17372733X-RAY DIFFRACTION100
1.48-1.520.21611310.16922729X-RAY DIFFRACTION100
1.52-1.550.17491440.16372766X-RAY DIFFRACTION100
1.55-1.60.16861380.16162741X-RAY DIFFRACTION99.97
1.6-1.640.17211400.16312771X-RAY DIFFRACTION99.97
1.64-1.70.18211460.16722753X-RAY DIFFRACTION100
1.7-1.760.18211390.17192778X-RAY DIFFRACTION99.97
1.76-1.830.16491180.16812784X-RAY DIFFRACTION100
1.83-1.910.19431470.16542772X-RAY DIFFRACTION100
1.91-2.010.1471410.16092782X-RAY DIFFRACTION100
2.01-2.140.17151520.16142794X-RAY DIFFRACTION100
2.14-2.30.1681320.15862826X-RAY DIFFRACTION100
2.3-2.530.19341490.16612807X-RAY DIFFRACTION100
2.53-2.90.16781720.17152818X-RAY DIFFRACTION100
2.9-3.650.19581590.16222885X-RAY DIFFRACTION100
3.65-23.140.13941640.15743044X-RAY DIFFRACTION99.81

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