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- PDB-5jkf: Crystal structure of esterase E22 -

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Basic information

Entry
Database: PDB / ID: 5jkf
TitleCrystal structure of esterase E22
ComponentsEsterase E22
KeywordsHYDROLASE / Esterase E32
Function / homologyhomoserine metabolic process / Homoserine/serine acetyltransferase MetX-like / homoserine O-acetyltransferase activity / methionine biosynthetic process / alpha/beta hydrolase fold / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Alpha/Beta hydrolase fold / cytoplasm / Probable acyltransferase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsZhang, Y. / Wang, P. / Yao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structural basis for substrate recognition and catalysis of a novel esterase E22 with a homoserine transacetylase-like fold
Authors: Zhang, Y. / Yao, Q. / Wang, P.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 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: Esterase E22
B: Esterase E22


Theoretical massNumber of molelcules
Total (without water)80,8832
Polymers80,8832
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-36 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.295, 67.682, 165.417
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 Esterase E22


Mass: 40441.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A1B1H1K0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1M CHES (pH 9.5), 16% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.393→42.75 Å / Num. obs: 24115 / % possible obs: 90.55 % / Redundancy: 3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 27.13
Reflection shellResolution: 2.393→2.478 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I1I

3i1i


Resolution: 2.393→42.749 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2524 1173 4.87 %
Rwork0.174 --
obs0.1779 24105 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.393→42.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 0 170 5844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085826
X-RAY DIFFRACTIONf_angle_d0.9547939
X-RAY DIFFRACTIONf_dihedral_angle_d13.3873437
X-RAY DIFFRACTIONf_chiral_restr0.054893
X-RAY DIFFRACTIONf_plane_restr0.0061026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3929-2.50180.36191370.22132828X-RAY DIFFRACTION90
2.5018-2.63360.28751470.21182849X-RAY DIFFRACTION91
2.6336-2.79860.2761450.20562843X-RAY DIFFRACTION92
2.7986-3.01460.29361440.19972859X-RAY DIFFRACTION92
3.0146-3.31790.33531320.19182842X-RAY DIFFRACTION90
3.3179-3.79780.2431640.16832805X-RAY DIFFRACTION89
3.7978-4.78380.211530.13522817X-RAY DIFFRACTION88
4.7838-42.75540.18081510.14763089X-RAY DIFFRACTION92

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