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- PDB-5dwd: Crystal structure of esterase PE8 -

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Basic information

Entry
Database: PDB / ID: 5dwd
TitleCrystal structure of esterase PE8
ComponentsEsterase
KeywordsHYDROLASE / Esterase / PE8
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPelagibacterium halotolerans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLi, J. / Huang, J.
CitationJournal: To Be Published
Title: Structure of esterase PE8
Authors: Li, J. / Huang, J.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3994
Polymers51,0542
Non-polymers3442
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-2 kcal/mol
Surface area18620 Å2
Unit cell
Length a, b, c (Å)41.772, 73.398, 66.403
Angle α, β, γ (deg.)90.00, 102.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Esterase / Phospholipase/carboxylesterase family protein


Mass: 25527.225 Da / Num. of mol.: 2 / Fragment: UNP residues 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacterium halotolerans (strain JCM 15775 / CGMCC 1.7692 / B2) (bacteria)
Strain: JCM 15775 / CGMCC 1.7692 / B2 / Gene: KKY_2995 / Production host: Escherichia coli (E. coli) / References: UniProt: G4RFI7, carboxylesterase
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M Calcium chloride dehydrate;0.1M BIS-TRIS pH 6.5;30%(v/v) Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.66→64.86 Å / Num. obs: 45616 / % possible obs: 99.1 % / Redundancy: 6.4 % / Net I/σ(I): 22.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→64.86 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.946 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 2304 5.1 %RANDOM
Rwork0.15583 ---
obs0.15813 43312 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-1.04 Å2
2--0.48 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.66→64.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 23 325 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193331
X-RAY DIFFRACTIONr_bond_other_d0.0020.023253
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9934546
X-RAY DIFFRACTIONr_angle_other_deg1.16137491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52523.782119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53315488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8571516
X-RAY DIFFRACTIONr_chiral_restr0.1680.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213735
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02689
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_it2.4182.2951749
X-RAY DIFFRACTIONr_mcbond_other2.4012.2931748
X-RAY DIFFRACTIONr_mcangle_it3.4493.432181
X-RAY DIFFRACTIONr_mcangle_other3.4563.4322182
X-RAY DIFFRACTIONr_scbond_it3.5472.6591582
X-RAY DIFFRACTIONr_scbond_other3.5442.6591582
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2313.8432366
X-RAY DIFFRACTIONr_long_range_B_refined7.39320.3343925
X-RAY DIFFRACTIONr_long_range_B_other7.39320.3353926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.658→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 149 -
Rwork0.194 2812 -
obs--87.06 %

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