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- PDB-9kho: Crystal structure of N-acyl homoserine lactonase AhlX mutant M41(... -

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Basic information

Entry
Database: PDB / ID: 9kho
TitleCrystal structure of N-acyl homoserine lactonase AhlX mutant M41(E77I/D177G/T243Y/H255L)
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: 2.16 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)176,01318
Polymers175,3096
Non-polymers70412
Water18,1771009
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.098, 149.830, 80.184
Angle α, β, γ (deg.)90.00, 109.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acylhomoserine lactonase


Mass: 29218.146 Da / Num. of mol.: 6 / Mutation: E77I/D157G/T243Y/H255L
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.: 12 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane (pH 6.5), and 20% w/v polyethylene glycol 3350
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: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.16→19.97 Å / Num. obs: 92605 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.8
Reflection shellResolution: 2.16→2.24 Å / Rmerge(I) obs: 0.083 / Num. unique obs: 92605

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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: 2.16→19.97 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 2010 2.17 %
Rwork0.1838 --
obs0.1847 92569 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11969 0 12 1009 12990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.882
X-RAY DIFFRACTIONf_dihedral_angle_d6.4821664
X-RAY DIFFRACTIONf_chiral_restr0.0541783
X-RAY DIFFRACTIONf_plane_restr0.0072183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.32711490.27086424X-RAY DIFFRACTION100
2.21-2.270.28771420.26216444X-RAY DIFFRACTION100
2.27-2.340.33691450.24366454X-RAY DIFFRACTION100
2.34-2.420.29271440.22896440X-RAY DIFFRACTION100
2.42-2.50.26891330.21776487X-RAY DIFFRACTION100
2.5-2.60.25771480.2076460X-RAY DIFFRACTION100
2.6-2.720.25971410.20396437X-RAY DIFFRACTION100
2.72-2.860.2891460.20276490X-RAY DIFFRACTION100
2.86-3.040.21791410.1966430X-RAY DIFFRACTION100
3.04-3.280.24591480.19226476X-RAY DIFFRACTION100
3.28-3.60.21581420.17076478X-RAY DIFFRACTION100
3.6-4.120.19611410.1536495X-RAY DIFFRACTION100
4.12-5.180.16291390.14116494X-RAY DIFFRACTION100
5.18-19.970.18491510.17026550X-RAY DIFFRACTION100

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