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- PDB-9khq: Crystal structure of N-acyl homoserine lactonase AhlX -

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Basic information

Entry
Database: PDB / ID: 9khq
TitleCrystal structure of N-acyl homoserine lactonase AhlX
ComponentsN-acylhomoserine lactonase
KeywordsHYDROLASE / Lactonase / Quorum sensing / Quorum quenching
Function / homology
Function and homology information


quorum-quenching N-acyl-homoserine lactonase / acyl-L-homoserine-lactone lactonohydrolase activity
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
NICKEL (II) ION / N-acylhomoserine lactonase
Similarity search - Component
Biological speciesSalinicola salarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, Y. / Chu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentGZC20232364 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: An AHL-lactonase mutant featuring a unique "tri-His" motif exhibits enhanced activity, stability and effectively controls plant soft rot.
Authors: Chen, Y. / Xie, X. / Zhou, J. / Dai, L. / Chu, X. / Liu, P.
History
DepositionNov 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acylhomoserine lactonase
B: N-acylhomoserine lactonase
C: N-acylhomoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14210
Polymers87,7653
Non-polymers3767
Water11,151619
1
A: N-acylhomoserine lactonase
B: N-acylhomoserine lactonase
C: N-acylhomoserine lactonase
hetero molecules

A: N-acylhomoserine lactonase
B: N-acylhomoserine lactonase
C: N-acylhomoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,28320
Polymers175,5306
Non-polymers75314
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area14190 Å2
ΔGint-197 kcal/mol
Surface area53070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.141, 143.141, 85.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-581-

HOH

31A-598-

HOH

41C-494-

HOH

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Components

#1: Protein N-acylhomoserine lactonase


Mass: 29255.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinicola salarius (bacteria) / Gene: ahlX / Production host: Escherichia coli (E. coli)
References: UniProt: A0A455K4F1, quorum-quenching N-acyl-homoserine lactonase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v polyethylene glycol 3350, 0.1 M Bis-Tris (pH 5.5), and 0.246 M MgCl2
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.2→19.98 Å / Num. obs: 45104 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.635 / Num. unique obs: 3861

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSv.1.04data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2000 4.44 %
Rwork0.1639 --
obs0.166 45025 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 7 619 6789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.937
X-RAY DIFFRACTIONf_dihedral_angle_d12.5132234
X-RAY DIFFRACTIONf_chiral_restr0.055914
X-RAY DIFFRACTIONf_plane_restr0.0091133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.28531400.21723020X-RAY DIFFRACTION100
2.26-2.320.28151410.20633041X-RAY DIFFRACTION100
2.32-2.380.26841420.19213034X-RAY DIFFRACTION100
2.38-2.460.23031400.18113019X-RAY DIFFRACTION100
2.46-2.550.21081420.1773065X-RAY DIFFRACTION100
2.55-2.650.25781420.18433044X-RAY DIFFRACTION99
2.65-2.770.26961420.18823055X-RAY DIFFRACTION100
2.77-2.920.22081420.18383052X-RAY DIFFRACTION100
2.92-3.10.22941430.17533073X-RAY DIFFRACTION100
3.1-3.340.20891420.16993065X-RAY DIFFRACTION99
3.34-3.670.17151450.15323103X-RAY DIFFRACTION100
3.67-4.20.15941440.13573117X-RAY DIFFRACTION100
4.2-5.270.17241460.12513123X-RAY DIFFRACTION99
5.27-19.980.19551490.15123214X-RAY DIFFRACTION97

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