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- PDB-5hc2: Structure of esterase Est22 mutant-S188A with p-nitrophenol -

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Basic information

Entry
Database: PDB / ID: 5hc2
TitleStructure of esterase Est22 mutant-S188A with p-nitrophenol
ComponentsLipolytic enzyme
KeywordsHYDROLASE / Esterase / Est22
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
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
IMIDAZOLE / P-NITROPHENOL / Lipolytic enzyme
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.986 Å
AuthorsLi, J. / Huang, J.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights of a hormone sensitive lipase homologue Est22.
Authors: Huang, J. / Huo, Y.Y. / Ji, R. / Kuang, S. / Ji, C. / Xu, X.W. / Li, J.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipolytic enzyme
B: Lipolytic enzyme
C: Lipolytic enzyme
D: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,16913
Polymers156,2674
Non-polymers9029
Water18,3751020
1
A: Lipolytic enzyme
B: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6197
Polymers78,1332
Non-polymers4855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint17 kcal/mol
Surface area23460 Å2
MethodPISA
2
C: Lipolytic enzyme
D: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5506
Polymers78,1332
Non-polymers4164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint14 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.646, 121.934, 150.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Lipolytic enzyme


Mass: 39066.684 Da / Num. of mol.: 4 / Mutation: S188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
References: UniProt: H6BDX1, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1M sodium citrate, 0.1M Imidazole, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 103730 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 25.76

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.986→46.332 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 5141 4.96 %
Rwork0.1528 --
obs0.1544 103555 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.986→46.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10255 0 65 1020 11340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610756
X-RAY DIFFRACTIONf_angle_d0.81214657
X-RAY DIFFRACTIONf_dihedral_angle_d14.0296463
X-RAY DIFFRACTIONf_chiral_restr0.0521589
X-RAY DIFFRACTIONf_plane_restr0.0051981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9858-2.00830.23661680.18192865X-RAY DIFFRACTION89
2.0083-2.0320.23631640.18483253X-RAY DIFFRACTION100
2.032-2.05670.22811510.1783276X-RAY DIFFRACTION100
2.0567-2.08280.23051770.17593248X-RAY DIFFRACTION100
2.0828-2.11020.22031820.16733264X-RAY DIFFRACTION100
2.1102-2.13910.20371670.16053258X-RAY DIFFRACTION100
2.1391-2.16970.1881560.15413268X-RAY DIFFRACTION100
2.1697-2.2020.2231770.16113273X-RAY DIFFRACTION100
2.202-2.23640.19961600.16173245X-RAY DIFFRACTION100
2.2364-2.27310.19861760.16083263X-RAY DIFFRACTION100
2.2731-2.31230.20441560.15673302X-RAY DIFFRACTION100
2.3123-2.35430.2241540.15493258X-RAY DIFFRACTION100
2.3543-2.39960.19011630.16013305X-RAY DIFFRACTION100
2.3996-2.44860.19351810.15673261X-RAY DIFFRACTION100
2.4486-2.50180.22331730.16743267X-RAY DIFFRACTION100
2.5018-2.560.20231650.1653290X-RAY DIFFRACTION100
2.56-2.62410.22851710.16553273X-RAY DIFFRACTION100
2.6241-2.6950.2071800.16343256X-RAY DIFFRACTION100
2.695-2.77430.20531770.16643288X-RAY DIFFRACTION100
2.7743-2.86380.19971800.16673274X-RAY DIFFRACTION100
2.8638-2.96620.20521910.1663274X-RAY DIFFRACTION100
2.9662-3.08490.19631750.16013301X-RAY DIFFRACTION100
3.0849-3.22530.2111580.16333330X-RAY DIFFRACTION100
3.2253-3.39530.19371780.15613304X-RAY DIFFRACTION100
3.3953-3.60790.17891600.14843309X-RAY DIFFRACTION100
3.6079-3.88630.16131850.13843352X-RAY DIFFRACTION100
3.8863-4.27720.14911770.12223326X-RAY DIFFRACTION100
4.2772-4.89550.1351570.12433371X-RAY DIFFRACTION100
4.8955-6.16560.15791860.14813386X-RAY DIFFRACTION100
6.1656-46.34470.14841960.15233474X-RAY DIFFRACTION98

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