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- PDB-5hc5: The structure of esterase Est22 mutant-S188A -

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Basic information

Entry
Database: PDB / ID: 5hc5
TitleThe structure of esterase Est22 mutant-S188A
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 / Resolution: 2.43 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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


Theoretical massNumber of molelcules
Total (without water)156,2674
Polymers156,2674
Non-polymers00
Water3,567198
1
A: Lipolytic enzyme
B: Lipolytic enzyme


Theoretical massNumber of molelcules
Total (without water)78,1332
Polymers78,1332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipolytic enzyme
D: Lipolytic enzyme


Theoretical massNumber of molelcules
Total (without water)78,1332
Polymers78,1332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.467, 121.802, 150.034
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.39 %
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: 2.43→94.56 Å / Num. obs: 55338 / % possible obs: 96.2 % / Redundancy: 5.4 % / Net I/σ(I): 8.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementResolution: 2.43→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.021 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22562 2476 5 %RANDOM
Rwork0.16124 ---
obs0.16447 47213 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10162 0 0 198 10360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910512
X-RAY DIFFRACTIONr_bond_other_d0.0020.029752
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.96714299
X-RAY DIFFRACTIONr_angle_other_deg0.994322548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57351396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20524.573457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.348151643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9161564
X-RAY DIFFRACTIONr_chiral_restr0.0840.21556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022278
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_it2.293.8785506
X-RAY DIFFRACTIONr_mcbond_other2.2873.8775505
X-RAY DIFFRACTIONr_mcangle_it3.5725.8086898
X-RAY DIFFRACTIONr_mcangle_other3.5725.8096899
X-RAY DIFFRACTIONr_scbond_it2.5324.0595006
X-RAY DIFFRACTIONr_scbond_other2.5324.0595006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0675.997391
X-RAY DIFFRACTIONr_long_range_B_refined5.56730.18411909
X-RAY DIFFRACTIONr_long_range_B_other5.54130.18411869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.434→2.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 72 -
Rwork0.272 1562 -
obs--39.66 %

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