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- PDB-5jkj: Crystal structure of esterase E22 L374D mutant -

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Basic information

Entry
Database: PDB / ID: 5jkj
TitleCrystal structure of esterase E22 L374D mutant
ComponentsEsterase E22
KeywordsHYDROLASE / Esterase E32
Function / homologyHomoserine/serine acetyltransferase MetX-like / acyltransferase activity, transferring groups other than amino-acyl groups / alpha/beta hydrolase fold / amino acid biosynthetic process / Alpha/beta hydrolase fold-1 / 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: 1.55 Å
AuthorsZhang, Y. / Wang, P. / Yao, Q.
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)80,8872
Polymers80,8872
Non-polymers00
Water15,655869
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-36 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.619, 68.898, 82.524
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Esterase E22


Mass: 40443.500 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.: 869 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 20% (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: Dec 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→35.394 Å / Num. obs: 94773 / % possible obs: 99.34 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.34
Reflection shellResolution: 1.55→1.606 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: 1.55→35.394 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 4757 5.02 %
Rwork0.1512 --
obs0.1526 94748 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→35.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 0 869 6559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065833
X-RAY DIFFRACTIONf_angle_d0.8127947
X-RAY DIFFRACTIONf_dihedral_angle_d11.2613441
X-RAY DIFFRACTIONf_chiral_restr0.055892
X-RAY DIFFRACTIONf_plane_restr0.0051029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.56780.19131270.15042844X-RAY DIFFRACTION94
1.5678-1.58620.20681580.15653052X-RAY DIFFRACTION100
1.5862-1.60550.1851580.15822955X-RAY DIFFRACTION100
1.6055-1.62590.22131620.15463016X-RAY DIFFRACTION100
1.6259-1.64730.18161630.15373000X-RAY DIFFRACTION100
1.6473-1.66980.20121550.15692994X-RAY DIFFRACTION100
1.6698-1.69370.18971530.14772958X-RAY DIFFRACTION100
1.6937-1.7190.19651810.14873019X-RAY DIFFRACTION100
1.719-1.74580.17981470.15792975X-RAY DIFFRACTION100
1.7458-1.77440.18461630.14833008X-RAY DIFFRACTION100
1.7744-1.8050.17161650.14982988X-RAY DIFFRACTION100
1.805-1.83790.18251510.15483035X-RAY DIFFRACTION100
1.8379-1.87320.19831360.14823011X-RAY DIFFRACTION100
1.8732-1.91140.18361570.15342981X-RAY DIFFRACTION100
1.9114-1.9530.19451580.15463022X-RAY DIFFRACTION100
1.953-1.99840.16511280.15293014X-RAY DIFFRACTION100
1.9984-2.04840.18721700.14862986X-RAY DIFFRACTION100
2.0484-2.10380.16671620.15393045X-RAY DIFFRACTION100
2.1038-2.16570.18721890.14862939X-RAY DIFFRACTION100
2.1657-2.23560.17961670.15452993X-RAY DIFFRACTION100
2.2356-2.31550.17881530.15652989X-RAY DIFFRACTION99
2.3155-2.40810.18381550.15362987X-RAY DIFFRACTION100
2.4081-2.51770.18731730.16183008X-RAY DIFFRACTION99
2.5177-2.65040.19761600.16553005X-RAY DIFFRACTION99
2.6504-2.81640.16971710.16332996X-RAY DIFFRACTION99
2.8164-3.03380.19651850.15612985X-RAY DIFFRACTION99
3.0338-3.33880.18211580.15463011X-RAY DIFFRACTION99
3.3388-3.82150.16661630.1383007X-RAY DIFFRACTION99
3.8215-4.81280.15391380.12853061X-RAY DIFFRACTION100
4.8128-35.40360.17181510.15623107X-RAY DIFFRACTION99

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