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- PDB-5egn: Est816 as an N-Acyl homoserine lactone degrading enzyme -

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Basic information

Entry
Database: PDB / ID: 5egn
TitleEst816 as an N-Acyl homoserine lactone degrading enzyme
ComponentsEsterase
KeywordsHYDROLASE / N-acyl-homoserine lactone / lactonase / quorum-sensing / thermostability
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
Similarity search - Function
Alpha/beta hydrolase family / Epoxide hydrolase-like / Alpha/beta hydrolase fold-1 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.636 Å
AuthorsXie, W. / Liu, X. / Cao, L. / Liu, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Guangdong Innovative Research Team Program2011Y038 China
The Fundamental Research Funds for the Central Universities15lgjc02 China
National Sciences Foundation of China31100579 China
Science and Technology Program of Guangzhou201504010025 China
CitationJournal: To Be Published
Title: Est816 as an N-Acyl homoserine lactone degrading enzyme
Authors: Xie, W. / Liu, X. / Cao, L. / Liu, Y.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
D: Esterase
E: Esterase
F: Esterase
G: Esterase
H: Esterase


Theoretical massNumber of molelcules
Total (without water)236,3148
Polymers236,3148
Non-polymers00
Water7,206400
1
A: Esterase
F: Esterase


Theoretical massNumber of molelcules
Total (without water)59,0782
Polymers59,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-18 kcal/mol
Surface area18600 Å2
MethodPISA
2
B: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)59,0782
Polymers59,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-18 kcal/mol
Surface area18450 Å2
MethodPISA
3
C: Esterase
E: Esterase


Theoretical massNumber of molelcules
Total (without water)59,0782
Polymers59,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-18 kcal/mol
Surface area18820 Å2
MethodPISA
4
G: Esterase
H: Esterase


Theoretical massNumber of molelcules
Total (without water)59,0782
Polymers59,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-18 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.806, 78.545, 116.472
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Esterase / AHL-lactonase 816


Mass: 29539.189 Da / Num. of mol.: 8 / Fragment: UNP residues 1-261 / Mutation: A216V/K238N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: est816 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6YRG4, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 28% PEG 3350, 0.1M sodium acetate pH 5.6, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 57955 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XUA

2xua


Resolution: 2.636→44.817 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 2981 5.2 %
Rwork0.2193 --
obs0.2216 57279 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.636→44.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15784 0 0 400 16184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316175
X-RAY DIFFRACTIONf_angle_d0.72922017
X-RAY DIFFRACTIONf_dihedral_angle_d13.8825712
X-RAY DIFFRACTIONf_chiral_restr0.0282425
X-RAY DIFFRACTIONf_plane_restr0.0042938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6362-2.67940.36371290.30282437X-RAY DIFFRACTION93
2.6794-2.72560.34251480.29172534X-RAY DIFFRACTION99
2.7256-2.77520.31761590.27872554X-RAY DIFFRACTION99
2.7752-2.82860.27751370.26982580X-RAY DIFFRACTION98
2.8286-2.88630.30811250.27422577X-RAY DIFFRACTION99
2.8863-2.9490.291440.26852562X-RAY DIFFRACTION99
2.949-3.01760.3261330.2552605X-RAY DIFFRACTION99
3.0176-3.09310.29771310.25422572X-RAY DIFFRACTION99
3.0931-3.17670.28821840.2492534X-RAY DIFFRACTION99
3.1767-3.27010.28511460.24312606X-RAY DIFFRACTION99
3.2701-3.37560.26231700.23452573X-RAY DIFFRACTION99
3.3756-3.49620.30951370.22742562X-RAY DIFFRACTION99
3.4962-3.63620.24221320.21642624X-RAY DIFFRACTION99
3.6362-3.80160.26751430.20752592X-RAY DIFFRACTION99
3.8016-4.00190.25631320.20142614X-RAY DIFFRACTION99
4.0019-4.25240.27341420.18622611X-RAY DIFFRACTION99
4.2524-4.58050.23161180.17952641X-RAY DIFFRACTION100
4.5805-5.04090.21751360.182632X-RAY DIFFRACTION99
5.0409-5.7690.20531340.19642641X-RAY DIFFRACTION100
5.769-7.26330.2511570.21372594X-RAY DIFFRACTION98
7.2633-44.82370.19791440.17682653X-RAY DIFFRACTION97

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