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- PDB-6kf1: Microbial Hormone-sensitive lipase- E53 mutant S162A -

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Basic information

Entry
Database: PDB / ID: 6kf1
TitleMicrobial Hormone-sensitive lipase- E53 mutant S162A
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANOIC ACID / P-NITROPHENOL / TRIETHYLENE GLYCOL / Lipase
Similarity search - Component
Biological speciesErythrobacter longus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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: Functional and Structural Insights into Environmental Adaptation of a Novel Hormone-sensitive Lipase, E53, Obtained from Erythrobacter longus
Authors: Xiaochen, Y. / Yingyi, H. / Zhengyang, L. / Shuling, J. / Zhen, R. / Zhao, W. / Xiaojian, H. / Henglin, C. / Jixi, L. / Xuewei, X.
History
DepositionJul 5, 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)133,31825
Polymers130,6084
Non-polymers2,71121
Water25,7431429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint26 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.394, 129.786, 220.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Lipase


Mass: 32623.162 Da / Num. of mol.: 3 / Mutation: S162A
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
#2: Protein Lipase


Mass: 32738.252 Da / Num. of mol.: 1 / Mutation: S162A
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 , 7 types, 1450 molecules

#3: Chemical
ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1429 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
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: 0.97776 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: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.996→48.701 Å / Num. obs: 136953 / % possible obs: 99.81 % / Redundancy: 13.2 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 42.633
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.357 / Num. unique obs: 13515

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPV

4ypv


Resolution: 1.996→48.701 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.525 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 6777 4.922 %
Rwork0.1589 --
all0.16 --
obs-136861 99.819 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.035 Å20 Å2-0 Å2
2---0.029 Å20 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.996→48.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9125 0 186 1429 10740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139505
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178977
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.64312953
X-RAY DIFFRACTIONr_angle_other_deg1.4611.56820705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61351233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.57520.812431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.399151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8751572
X-RAY DIFFRACTIONr_chiral_restr0.0920.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021973
X-RAY DIFFRACTIONr_nbd_refined0.210.22143
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.28795
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.21169
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1570.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0810.24
X-RAY DIFFRACTIONr_nbd_other0.1760.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.224
X-RAY DIFFRACTIONr_mcbond_it3.0853.1814954
X-RAY DIFFRACTIONr_mcbond_other3.0653.1794949
X-RAY DIFFRACTIONr_mcangle_it3.5174.7466178
X-RAY DIFFRACTIONr_mcangle_other3.5194.7466177
X-RAY DIFFRACTIONr_scbond_it3.8293.5014551
X-RAY DIFFRACTIONr_scbond_other3.8293.5014552
X-RAY DIFFRACTIONr_scangle_it5.145.1286775
X-RAY DIFFRACTIONr_scangle_other5.145.1286776
X-RAY DIFFRACTIONr_lrange_it6.50941.38411327
X-RAY DIFFRACTIONr_lrange_other6.44841.13711219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.996-2.0480.2294720.1949485X-RAY DIFFRACTION99.1239
2.048-2.1040.2144670.1769373X-RAY DIFFRACTION99.9797
2.104-2.1650.2254410.1759109X-RAY DIFFRACTION99.9686
2.165-2.2310.214910.1678825X-RAY DIFFRACTION99.9464
2.231-2.3040.2014490.1568566X-RAY DIFFRACTION99.9557
2.304-2.3850.2094180.1528308X-RAY DIFFRACTION99.9542
2.385-2.4750.2044100.1578018X-RAY DIFFRACTION99.9526
2.475-2.5760.1994140.1487707X-RAY DIFFRACTION99.9508
2.576-2.6910.1893980.1527442X-RAY DIFFRACTION99.9363
2.691-2.8220.23880.1527094X-RAY DIFFRACTION99.9866
2.822-2.9740.1963410.1656740X-RAY DIFFRACTION99.9718
2.974-3.1550.213260.1756441X-RAY DIFFRACTION99.9409
3.155-3.3720.183270.1746027X-RAY DIFFRACTION99.89
3.372-3.6420.1963050.175619X-RAY DIFFRACTION99.8988
3.642-3.990.1842480.1545221X-RAY DIFFRACTION99.7083
3.99-4.460.1482450.1264725X-RAY DIFFRACTION99.6991
4.46-5.1480.1572380.134165X-RAY DIFFRACTION99.5703
5.148-6.3020.1731690.1563598X-RAY DIFFRACTION99.8674
6.302-8.8980.1631510.1512832X-RAY DIFFRACTION99.7993
8.898-48.7010.246790.2161626X-RAY DIFFRACTION97.2618

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