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- PDB-6kf7: Microbial Hormone-sensitive lipase E53 mutant S285G -

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Basic information

Entry
Database: PDB / ID: 6kf7
TitleMicrobial Hormone-sensitive lipase E53 mutant S285G
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANOIC ACID / (4-nitrophenyl) hexanoate / P-NITROPHENOL / TRIETHYLENE GLYCOL / Lipase
Similarity search - Component
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXiaochen, Y. / Zhengyang, L. / Xuewei, X. / Jixi, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31770004 China
CitationJournal: To Be Published
Title: Microbial Hormone-sensitive lipase E53 mutant S285G
Authors: Xiaochen, Y.
History
DepositionJul 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)136,45843
Polymers132,5154
Non-polymers3,94339
Water25,3831409
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,34914
Polymers33,1291
Non-polymers1,22013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7667
Polymers33,1291
Non-polymers6386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,18711
Polymers33,1291
Non-polymers1,05810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,15611
Polymers33,1291
Non-polymers1,02710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.657, 129.715, 219.464
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)
Components on special symmetry positions
IDModelComponents
11B-782-

HOH

21B-794-

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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A074MDU6

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Non-polymers , 8 types, 1448 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-6NA / HEXANOIC ACID / Caproic acid


Mass: 116.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1409 / 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: 67.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Calcium chloride, Bis-Tris, PEG MME 550, pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.8→48.53 Å / Num. obs: 186934 / % possible obs: 99.62 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.48 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 21.756
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.548 / Num. unique obs: 18389

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Processing

Software
NameClassification
PHENIXrefinement
SCALEPACKdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 1.8→48.53 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9413
RfactorNum. reflection% reflection
Rfree0.1909 9409 5.03 %
Rwork0.1686 --
obs0.1699 186898 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 262 1409 10785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659545
X-RAY DIFFRACTIONf_angle_d0.833112956
X-RAY DIFFRACTIONf_chiral_restr0.05231471
X-RAY DIFFRACTIONf_plane_restr0.00581708
X-RAY DIFFRACTIONf_dihedral_angle_d8.3095709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.28172970.26695583X-RAY DIFFRACTION95.07
1.82-1.840.27073060.24895826X-RAY DIFFRACTION99.58
1.84-1.860.26033130.23585880X-RAY DIFFRACTION99.29
1.86-1.890.23283220.22295798X-RAY DIFFRACTION99.67
1.89-1.910.24822890.22085905X-RAY DIFFRACTION99.45
1.91-1.940.24052930.22565855X-RAY DIFFRACTION99.74
1.94-1.960.25313150.21365869X-RAY DIFFRACTION99.49
1.96-1.990.24233100.20455859X-RAY DIFFRACTION99.69
1.99-2.020.21883080.19085874X-RAY DIFFRACTION99.63
2.02-2.060.21672870.18735873X-RAY DIFFRACTION99.55
2.06-2.090.21753330.18965843X-RAY DIFFRACTION99.52
2.09-2.130.23383020.19185904X-RAY DIFFRACTION99.86
2.13-2.170.20653210.18265857X-RAY DIFFRACTION99.89
2.17-2.220.21193250.18095902X-RAY DIFFRACTION99.92
2.22-2.270.2033350.17475866X-RAY DIFFRACTION99.95
2.27-2.320.20033100.17265921X-RAY DIFFRACTION99.94
2.32-2.380.20293050.17755910X-RAY DIFFRACTION99.95
2.38-2.440.19642980.17555935X-RAY DIFFRACTION99.95
2.44-2.510.21372940.17535941X-RAY DIFFRACTION99.95
2.51-2.590.20363550.17295906X-RAY DIFFRACTION100
2.59-2.690.1963370.16915878X-RAY DIFFRACTION99.98
2.69-2.790.20473230.16645929X-RAY DIFFRACTION100
2.79-2.920.20083280.16735946X-RAY DIFFRACTION99.98
2.92-3.070.18613210.16695994X-RAY DIFFRACTION99.98
3.07-3.270.18753150.15745936X-RAY DIFFRACTION99.98
3.27-3.520.17513010.15196012X-RAY DIFFRACTION99.97
3.52-3.870.16273250.14445991X-RAY DIFFRACTION99.98
3.87-4.430.14563420.13416045X-RAY DIFFRACTION99.97
4.43-5.580.1572840.14546122X-RAY DIFFRACTION99.91
5.58-48.530.17773150.17226329X-RAY DIFFRACTION99.13

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