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- PDB-5hc4: Structure of esterase Est22 -

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Basic information

Entry
Database: PDB / ID: 5hc4
TitleStructure 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 / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5456
Polymers156,3314
Non-polymers2142
Water20,3751131
1
A: Lipolytic enzyme
B: Lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3804
Polymers78,1652
Non-polymers2142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipolytic enzyme
D: Lipolytic enzyme


Theoretical massNumber of molelcules
Total (without water)78,1652
Polymers78,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.243, 121.811, 150.522
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: 39082.684 Da / Num. of mol.: 4
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1131 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES Sodium, pH7.5, 1.5M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 101542 / % possible obs: 100 % / Redundancy: 12.5 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.781 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.23275 4786 5 %RANDOM
Rwork0.17392 ---
obs0.17681 91396 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--1.18 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10183 0 14 1131 11328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.96614123
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79751361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79224.549455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.547151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7411564
X-RAY DIFFRACTIONr_chiral_restr0.1280.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218024
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.9323.0965454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9454.626808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2193.2894954
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.97526.97117703
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 280 -
Rwork0.232 5334 -
obs--75.72 %

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