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- PDB-3dhc: 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase wit... -

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Basic information

Entry
Database: PDB / ID: 3dhc
Title1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to The catalytic Metal Center
ComponentsN-Acyl Homoserine Lactone Hydrolase
KeywordsHYDROLASE / Zinc Bimetallohydrolase / Qourum Quenching / N-Acyl Homocysteine Thiolactone / Product Complex / AHL Lactonase / General Acid / Catalytic Mechanism
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 / 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
N-hexanoyl-L-homocysteine / 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: 1.3 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 thuringiensis: 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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)29,58110
Polymers28,6651
Non-polymers9179
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.775, 55.460, 79.191
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: TEV protease was used to cut off the fusion protein MBP resulting in 4 extra residues at the N terminus. The extra residues are not observed in the structure
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-CYK / N-hexanoyl-L-homocysteine


Mass: 233.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19NO3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 41.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Glycerol, Tris-HCl, MgCl2, N-Hexanoyl-L-Homocysteine Thiolactone, Methanol, 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: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2006 / Details: K-B pair biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 60162 / Num. obs: 56793 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.5
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A7M

2a7m


Resolution: 1.3→23.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.615 / SU ML: 0.03 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2869 5.1 %RANDOM
Rwork0.143 ---
obs0.145 53865 94.4 %-
all-60162 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.048 Å
Refinement stepCycle: LAST / Resolution: 1.3→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 53 271 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.052.0032914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45225.15597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.579157
X-RAY DIFFRACTIONr_chiral_restr0.2670.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021587
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21504
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4651.51309
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33122095
X-RAY DIFFRACTIONr_scbond_it4.9653941
X-RAY DIFFRACTIONr_scangle_it6.6224.5818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 123 -
Rwork0.306 2719 -
obs--65.11 %

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