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- PDB-7cih: Microbial Hormone-sensitive lipase E53 mutant S285G -

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Basic information

Entry
Database: PDB / ID: 7cih
TitleMicrobial Hormone-sensitive lipase E53 mutant S285G
ComponentsLipase
KeywordsHYDROLASE / Esterase / Microbial Hormone-sensitive lipase
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / (4-nitrophenyl) hexanoate / 1,4-DIETHYLENE DIOXIDE / P-NITROPHENOL / Lipase
Function and homology information
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 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
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,34057
Polymers132,5154
Non-polymers4,82653
Water22,5371251
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,25114
Polymers33,1291
Non-polymers1,12213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68118
Polymers33,1291
Non-polymers1,55317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,16912
Polymers33,1291
Non-polymers1,04011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,23913
Polymers33,1291
Non-polymers1,11012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.664, 129.692, 219.567
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11D-509-

DIO

21D-509-

DIO

31B-666-

HOH

41B-889-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lipase


Mass: 33128.703 Da / Num. of mol.: 4 / Mutation: S285G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter longus (bacteria) / Gene: EH31_02760 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A074MDU6

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Non-polymers , 8 types, 1304 molecules

#2: 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
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#7: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.8 Å3/Da / Density % sol: 67.6 %
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: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.789→48.54 Å / Num. obs: 189466 / % possible obs: 99.47 % / Redundancy: 2 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02048 / Net I/σ(I): 18.53
Reflection shellResolution: 1.789→1.853 Å / Rmerge(I) obs: 0.3826 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 18072 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 1.789→48.54 Å / Cross valid method: FREE R-VALUE
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1901 9460 -
Rwork0.169 --
obs-189466 99.47 %
Displacement parametersBiso mean: 35.88 Å2
Refinement stepCycle: LAST / Resolution: 1.789→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 306 1251 10685
LS refinement shellResolution: 1.789→1.853 Å
RfactorNum. reflection% reflection
Rfree0.3254 --
Rwork0.3035 18072 -
obs--95.93 %

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