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- PDB-5hc3: The structure of esterase Est22 -

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Basic information

Entry
Database: PDB / ID: 5hc3
TitleThe structure of esterase Est22
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
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Nov 8, 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

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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)156,6358
Polymers156,2674
Non-polymers3684
Water10,106561
1
A: Lipolytic enzyme
B: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4105
Polymers78,1332
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipolytic enzyme
D: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2253
Polymers78,1332
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.160, 121.679, 150.490
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: S170A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2M Sodium tartrate dihydrate, pH7.3, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 58728 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 17.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HC4

5hc4


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.685 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2942 5 %RANDOM
Rwork0.13743 ---
obs0.14031 55582 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.078 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å20 Å2
2--1.21 Å2-0 Å2
3----3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10144 0 24 561 10729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910551
X-RAY DIFFRACTIONr_bond_other_d0.0020.029796
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.96814357
X-RAY DIFFRACTIONr_angle_other_deg1.017322651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44851403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85624.585458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.769151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1611564
X-RAY DIFFRACTIONr_chiral_restr0.0940.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.553.6015516
X-RAY DIFFRACTIONr_mcbond_other2.5483.6015515
X-RAY DIFFRACTIONr_mcangle_it3.8235.3876918
X-RAY DIFFRACTIONr_mcangle_other3.8235.3886919
X-RAY DIFFRACTIONr_scbond_it3.3043.8725035
X-RAY DIFFRACTIONr_scbond_other3.3013.8725035
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0155.6787429
X-RAY DIFFRACTIONr_long_range_B_refined6.42528.74312290
X-RAY DIFFRACTIONr_long_range_B_other6.33428.56912058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 223 -
Rwork0.18 3885 -
obs--95.89 %

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