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Basic information

Entry
Database: PDB / ID: 5eh9
TitleIndirect contributions of mutations underlie optimization of new enzyme function
ComponentsN-acyl homoserine lactonase AiiA
KeywordsHYDROLASE / N-Acyl homoserine lactonase from Bacillus thuringiensis
Function / homology
Function and homology information


quorum-quenching N-acyl-homoserine lactonase / acyl-L-homoserine-lactone lactonohydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-HYDROXYETHYL DISULFIDE / N-acyl homoserine lactonase AiiA
Similarity search - Component
Biological speciesBacillus thuringiensis subsp. kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsHong, N.-S. / Jackson, C.J. / Tokuriki, N. / Yang, G. / Baier, F.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acyl homoserine lactonase AiiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,43211
Polymers28,5021
Non-polymers93010
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.511, 55.473, 79.358
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 AiiA / AHL-lactonase AiiA


Mass: 28502.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis subsp. kurstaki (bacteria)
Gene: aiiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0CJ63, 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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
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→45.47 Å / Num. obs: 61128 / % possible obs: 99.8 % / Redundancy: 7 % / Net I/σ(I): 16.33

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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 3DHB

3dhb


Resolution: 1.29→45.47 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.898 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15347 3094 5.1 %RANDOM
Rwork0.11503 ---
obs0.11693 58033 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0 Å2
2--1.5 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.29→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 52 259 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192211
X-RAY DIFFRACTIONr_bond_other_d0.0020.022084
X-RAY DIFFRACTIONr_angle_refined_deg2.2441.992985
X-RAY DIFFRACTIONr_angle_other_deg1.3673.0014843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14424.94999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11115374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.889158
X-RAY DIFFRACTIONr_chiral_restr0.1630.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212475
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02473
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_it3.8832.0211065
X-RAY DIFFRACTIONr_mcbond_other3.8832.0211064
X-RAY DIFFRACTIONr_mcangle_it4.6523.0531347
X-RAY DIFFRACTIONr_mcangle_other4.6513.0531348
X-RAY DIFFRACTIONr_scbond_it6.0272.5481146
X-RAY DIFFRACTIONr_scbond_other6.0272.551147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6883.6121639
X-RAY DIFFRACTIONr_long_range_B_refined7.61619.0862627
X-RAY DIFFRACTIONr_long_range_B_other7.61519.1042628
X-RAY DIFFRACTIONr_rigid_bond_restr6.80934295
X-RAY DIFFRACTIONr_sphericity_free54.8587
X-RAY DIFFRACTIONr_sphericity_bonded20.74354410
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 221 -
Rwork0.252 4245 -
obs--99.82 %

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