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- PDB-3dha: An Ultral High Resolution Structure of N-Acyl Homoserine Lactone ... -

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Basic information

Entry
Database: PDB / ID: 3dha
TitleAn Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site
ComponentsN-Acyl Homoserine Lactone Hydrolase
KeywordsHYDROLASE / Zinc Bimetallohydrolase / Quorum Quenching / N-Acyl Homoserine lactone / Alternative Binding Site / Product Complex / AHL Lactonase
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-hexanoyl-L-homoserine / N-acyl homoserine lactonase AiiA / N-acyl homoserine lactonase
Similarity search - Component
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsLiu, D. / Momb, J. / Thomas, P.W. / Moulin, A. / Petsko, G.A. / Fast, W. / Ringe, D.
Citation
Journal: Biochemistry / Year: 2008
Title: Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.
Authors: Liu, D. / Momb, J. / Thomas, P.W. / Moulin, A. / Petsko, G.A. / Fast, W. / Ringe, D.
#1: Journal: To be Published
Title: Mechanism of the Quorum-quenching Lactonase (AiiA) from Bacillus thuringensis: 2. Substrate Modeling and Active Site Mutations
Authors: Momb, J. / Wang, C. / Liu, D. / Thomas, P.W. / Petsko, G.A. / Guo, H. / Ringe, D. / Fast, W.
History
DepositionJun 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-Acyl Homoserine Lactone Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3818
Polymers28,6651
Non-polymers7167
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.929, 55.604, 78.703
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 Lactone Hydrolase / AiiA-like protein


Mass: 28664.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria)
Description: The fusion protein, maltose binding protein, was cut off before crystallization using TEV protease resulting in 4 extra residues at the N terminus.
Gene: aiiA / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7B8B9, UniProt: P0CJ63*PLUS, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C6L / N-hexanoyl-L-homoserine


Mass: 217.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19NO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 41.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Glycerol, Tris-HCl, PEG4000, MgCl2, N-hexanoyl-L-homoserine lactone, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2006 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 141032 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / Num. unique all: 9081 / % possible all: 61.9

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
Blu-IceIcedata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A7M

2a7m


Resolution: 0.95→45 Å / Num. parameters: 22638 / Num. restraintsaints: 28771 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0565
RfactorNum. reflection% reflectionSelection details
Rfree0.169 7051 -RANDOM
Rwork0.1327 ---
all0.1327 150193 --
obs0.1327 141032 93.9 %-
Displacement parametersBiso mean: 21.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.037 Å / Num. disordered residues: 18 / Occupancy sum hydrogen: 1951 / Occupancy sum non hydrogen: 2406.5
Refinement stepCycle: LAST / Resolution: 0.95→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 41 255 2314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0314
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.11
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.058
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.11
LS refinement shellResolution: 0.95→0.98 Å /
Num. reflection% reflection
obs9081 0.61 %

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