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Basic information

Entry
Database: PDB / ID: 5eht
TitleIndirect contributions of mutations underlie optimization of new enzyme function
ComponentsN-acyl homoserine lactonase
KeywordsHYDROLASE / N-Acyl-Homoserine Lactonase / Directed evolution / AiiA / QQL / Lactonase / Phosphatase / Paraoxonase
Function / homology
Function and homology information


lactone catabolic process / quorum-quenching N-acyl-homoserine lactonase / acyl-L-homoserine-lactone lactonohydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acyl homoserine lactonase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsJackson, C.J. / Hong, N.-S.
CitationJournal: Biochemistry / Year: 2016
Title: Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects.
Authors: Yang, G. / Hong, N. / Baier, F. / Jackson, C.J. / Tokuriki, N.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acyl homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1529
Polymers28,4681
Non-polymers6838
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.638, 55.735, 79.878
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 N-acyl homoserine lactonase / AHL-lactonase / Homoserine lactone lactonase


Mass: 28468.330 Da / Num. of mol.: 1 / Mutation: I9V, S20F, L33V, F64(CSO), V69G, K139T, I230M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: aiiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3FJ64, quorum-quenching N-acyl-homoserine lactonase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 4 K, 20% (v/v) glycerol, 80 mM Tris-HCl, pH 8.5, 160 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.29→32.49 Å / Num. obs: 61760 / % possible obs: 99.47 % / Redundancy: 13.4 % / Net I/σ(I): 20.78

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EH9

5eh9


Resolution: 1.29→32.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.743 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16805 3132 5.1 %RANDOM
Rwork0.12581 ---
obs0.12796 58628 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2--1.24 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.29→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 38 247 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192202
X-RAY DIFFRACTIONr_bond_other_d0.0020.022058
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.9882982
X-RAY DIFFRACTIONr_angle_other_deg1.29234787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80925.15299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.563157
X-RAY DIFFRACTIONr_chiral_restr0.1430.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212486
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02469
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_it3.221.7891073
X-RAY DIFFRACTIONr_mcbond_other3.2151.7881072
X-RAY DIFFRACTIONr_mcangle_it3.7912.7061357
X-RAY DIFFRACTIONr_mcangle_other3.7912.7071358
X-RAY DIFFRACTIONr_scbond_it5.4852.2871129
X-RAY DIFFRACTIONr_scbond_other5.4922.2871129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0623.2521626
X-RAY DIFFRACTIONr_long_range_B_refined8.87517.2822610
X-RAY DIFFRACTIONr_long_range_B_other8.87517.2752610
X-RAY DIFFRACTIONr_rigid_bond_restr6.45134260
X-RAY DIFFRACTIONr_sphericity_free72.304575
X-RAY DIFFRACTIONr_sphericity_bonded20.87154372
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 207 -
Rwork0.307 4285 -
obs--99.1 %

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