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

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Basic information

Entry
Database: PDB / ID: 7cip
TitleMicrobial Hormone-sensitive lipase E53 wild type
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 / 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: 1.752 Å
AuthorsYang, X. / Li, Z. / Xu, X. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770004 China
CitationJournal: To Be Published
Title: Microbial Hormone-sensitive lipase E53 wild type
Authors: Yang, X.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)139,35592
Polymers132,6354
Non-polymers6,72088
Water25,8151433
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,72021
Polymers33,1591
Non-polymers1,56120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,01425
Polymers33,1591
Non-polymers1,85524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77222
Polymers33,1591
Non-polymers1,61321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,85024
Polymers33,1591
Non-polymers1,69123
Water181
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
Components on special symmetry positions
IDModelComponents
11D-1421-

NPO

21D-1421-

NPO

31D-1421-

NPO

41D-1421-

NPO

51B-744-

HOH

61B-1010-

HOH

71D-1661-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lipase


Mass: 33158.730 Da / Num. of mol.: 4
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, 1521 molecules

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


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


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


Mass: 116.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 41.052 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H3N
#7: 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
#8: Chemical ChemComp-SO4 / SULFATE ION


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


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


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


Mass: 139.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5NO3
#12: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1433 / 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: 3.82 Å3/Da / Density % sol: 67.79 %
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: 1.752→48.71 Å / Num. obs: 203688 / % possible obs: 99.86 % / Redundancy: 2 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 14.19
Reflection shellResolution: 1.752→1.815 Å / Num. unique obs: 20074 / CC1/2: 0.849 / CC star: 0.958

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Processing

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

4ypv


Resolution: 1.752→48.71 Å / Cross valid method: FREE R-VALUE
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1811 --
Rwork0.1764 --
obs-203688 99.85 %
Displacement parametersBiso mean: 31.71 Å2
Refinement stepCycle: LAST / Resolution: 1.752→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 439 1433 11012

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