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- PDB-7w8n: Microbial Hormone-sensitive lipase E53 wild type -

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Basic information

Entry
Database: PDB / ID: 7w8n
TitleMicrobial Hormone-sensitive lipase E53 wild type
Components(Lipase) x 2
KeywordsHYDROLASE / Esterase / Microbial Hormone-sensitive lipase
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
HEXANOIC ACID / butanoic acid / ACETONITRILE / (4-nitrophenyl) hexanoate / 1,4-DIETHYLENE DIOXIDE / P-NITROPHENOL / Lipase
Similarity search - Component
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYang, X. / Li, Z. / Xu, X. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770004 China
CitationJournal: Front Microbiol / Year: 2021
Title: Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus .
Authors: Ding, Y. / Nie, L. / Yang, X.C. / Li, Y. / Huo, Y.Y. / Li, Z. / Gao, Y. / Cui, H.L. / Li, J. / Xu, X.W.
History
DepositionDec 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details
Item: _pdbx_database_related.content_type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
B: Lipase
C: Lipase
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,29792
Polymers132,5774
Non-polymers6,72088
Water25,7791431
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.576, 129.838, 221.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11D-421-

NPO

21D-421-

NPO

31D-421-

NPO

41D-421-

NPO

51B-758-

HOH

61B-969-

HOH

71D-1655-

HOH

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Lipase


Mass: 33158.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A074MDU6
#2: Protein Lipase


Mass: 33100.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A074MDU6

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Non-polymers , 12 types, 1519 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical...
ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H3N
#8: Chemical
ChemComp-D8F / (4-nitrophenyl) hexanoate


Mass: 237.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#11: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#12: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1431 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: MES pH 6.5, PEG, ammonium sulfate, dioxane, PEG 1000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→48.71 Å / Num. obs: 203632 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 14.19
Reflection shellResolution: 1.75→1.815 Å / Num. unique obs: 20063 / CC1/2: 0.849 / CC star: 0.958

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.18refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 1.75→48.71 Å / SU ML: 0.186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1786 10276 5.05 %
Rwork0.1641 193356 -
obs0.1648 203632 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 439 1431 11006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01169699
X-RAY DIFFRACTIONf_angle_d1.169613086
X-RAY DIFFRACTIONf_chiral_restr0.15051476
X-RAY DIFFRACTIONf_plane_restr0.00841715
X-RAY DIFFRACTIONf_dihedral_angle_d14.23013486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.323220.31746344X-RAY DIFFRACTION98.43
1.77-1.790.28993500.27736323X-RAY DIFFRACTION99.94
1.79-1.820.27212970.25626428X-RAY DIFFRACTION99.97
1.82-1.840.25233420.24576350X-RAY DIFFRACTION99.94
1.84-1.860.26093470.23016438X-RAY DIFFRACTION99.93
1.86-1.890.28033530.22136364X-RAY DIFFRACTION99.96
1.89-1.910.22363530.21056403X-RAY DIFFRACTION100
1.91-1.940.22023480.20366363X-RAY DIFFRACTION99.99
1.94-1.970.22023360.19926413X-RAY DIFFRACTION99.99
1.97-2.010.20483570.19276378X-RAY DIFFRACTION99.88
2.01-2.040.21223450.1916374X-RAY DIFFRACTION100
2.04-2.080.20113580.18786433X-RAY DIFFRACTION100
2.08-2.120.21553370.1916367X-RAY DIFFRACTION99.97
2.12-2.160.20662960.17836455X-RAY DIFFRACTION99.94
2.16-2.210.19613370.17816452X-RAY DIFFRACTION99.97
2.21-2.260.19373410.17056390X-RAY DIFFRACTION100
2.26-2.320.16743220.16416442X-RAY DIFFRACTION100
2.32-2.380.18113310.16266434X-RAY DIFFRACTION99.99
2.38-2.450.18933750.16746431X-RAY DIFFRACTION99.99
2.45-2.530.17773350.16476448X-RAY DIFFRACTION99.99
2.53-2.620.18413510.16246460X-RAY DIFFRACTION100
2.62-2.720.18473500.16066421X-RAY DIFFRACTION100
2.72-2.850.17993450.15726474X-RAY DIFFRACTION99.99
2.85-30.1583260.16176457X-RAY DIFFRACTION100
3-3.180.18183500.16466507X-RAY DIFFRACTION99.91
3.18-3.430.17053750.15796477X-RAY DIFFRACTION99.96
3.43-3.770.15323330.14366537X-RAY DIFFRACTION99.93
3.77-4.320.13693660.13036547X-RAY DIFFRACTION99.93
4.32-5.440.13953600.1226638X-RAY DIFFRACTION99.89
5.44-48.710.17873380.1696808X-RAY DIFFRACTION98.58

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