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- PDB-7ci0: Microbial Hormone-sensitive lipase E53 mutant S162A -

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Basic information

Entry
Database: PDB / ID: 7ci0
TitleMicrobial Hormone-sensitive lipase E53 mutant S162A
ComponentsLipase
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 / 1,4-DIETHYLENE DIOXIDE / P-NITROPHENOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lipase
Similarity search - Component
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 6, 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

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)138,73368
Polymers132,5714
Non-polymers6,16264
Water24,5181361
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,90819
Polymers33,1431
Non-polymers1,76518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,62718
Polymers33,1431
Non-polymers1,48517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,69517
Polymers33,1431
Non-polymers1,55316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,50214
Polymers33,1431
Non-polymers1,36013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.397, 129.771, 220.661
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-812-

NPO

21D-812-

NPO

31D-812-

NPO

41B-2843-

HOH

51B-3092-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lipase


Mass: 33142.730 Da / Num. of mol.: 4 / Mutation: S162A
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 , 12 types, 1425 molecules

#2: Chemical
ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#12: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1361 / 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: 67.64 %
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: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.7→48.66 Å / Num. obs: 221017 / % possible obs: 99.79 % / Redundancy: 2 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.015 / Net I/σ(I): 20.16
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 21745 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
PHENIX1.14_3247refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 1.7→47.35 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2447 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1908 11063 5.01 %
Rwork0.1711 209779 -
obs0.1723 221017 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 392 1361 10881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01079678
X-RAY DIFFRACTIONf_angle_d1.000813119
X-RAY DIFFRACTIONf_chiral_restr0.06741478
X-RAY DIFFRACTIONf_plane_restr0.00641715
X-RAY DIFFRACTIONf_dihedral_angle_d17.10323453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.36283110.33026796X-RAY DIFFRACTION96.51
1.72-1.740.28483460.26226892X-RAY DIFFRACTION99.82
1.74-1.760.2583350.24787008X-RAY DIFFRACTION99.81
1.76-1.790.27663540.24676890X-RAY DIFFRACTION99.81
1.79-1.810.25823460.23446967X-RAY DIFFRACTION99.82
1.81-1.830.26143720.22746902X-RAY DIFFRACTION99.85
1.83-1.860.24583550.21446958X-RAY DIFFRACTION99.86
1.86-1.890.24053570.20566923X-RAY DIFFRACTION99.89
1.89-1.920.21563690.19986968X-RAY DIFFRACTION99.93
1.92-1.950.22073710.19626941X-RAY DIFFRACTION99.92
1.95-1.980.22683570.19386944X-RAY DIFFRACTION99.92
1.98-2.020.21013540.19076977X-RAY DIFFRACTION99.8
2.02-2.060.21293700.19456950X-RAY DIFFRACTION99.89
2.06-2.10.214000.19066898X-RAY DIFFRACTION99.92
2.1-2.140.21953810.18976985X-RAY DIFFRACTION99.88
2.14-2.190.21114060.18666920X-RAY DIFFRACTION99.85
2.19-2.250.20183560.18156988X-RAY DIFFRACTION99.89
2.25-2.310.21863590.17616954X-RAY DIFFRACTION99.81
2.31-2.380.20043810.17086969X-RAY DIFFRACTION99.88
2.38-2.450.19994020.17076982X-RAY DIFFRACTION99.88
2.45-2.540.20343700.1736991X-RAY DIFFRACTION99.86
2.54-2.640.19393950.1736945X-RAY DIFFRACTION99.89
2.64-2.760.19893710.16877033X-RAY DIFFRACTION99.88
2.76-2.910.19223670.17337026X-RAY DIFFRACTION99.96
2.91-3.090.19483810.17737040X-RAY DIFFRACTION99.95
3.09-3.330.19523580.17327060X-RAY DIFFRACTION99.97
3.33-3.670.1743680.15747102X-RAY DIFFRACTION99.95
3.67-4.20.15393920.14357119X-RAY DIFFRACTION100
4.2-5.290.13463890.13167174X-RAY DIFFRACTION99.95
5.29-47.350.18983900.16837477X-RAY DIFFRACTION99.89

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