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- PDB-1kzf: Crystal Structure of the Acyl-homoserine Lactone Synthase, EsaI -

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Basic information

Entry
Database: PDB / ID: 1kzf
TitleCrystal Structure of the Acyl-homoserine Lactone Synthase, EsaI
Componentsacyl-homoserinelactone synthase EsaI
KeywordsLIGASE / alpha-beta / autoinducer synthase / acylhomoserine lactone / quorum sensing / bacterial pathogenesis
Function / homology
Function and homology information


acyl-homoserine-lactone synthase / N-acyl homoserine lactone synthase activity / quorum sensing / signal transduction
Similarity search - Function
Autoinducer synthesis, conserved site / Autoinducer synthase family signature. / Autoinducer synthase / Autoinducer synthase / Autoinducer synthase family profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acyl-homoserine-lactone synthase
Similarity search - Component
Biological speciesPantoea stewartii subsp. stewartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWatson, W.T. / Minogue, T.D. / Val, D.L. / Beck von Bodman, S. / Churchill, M.E.A.
Citation
Journal: Mol.Cell / Year: 2002
Title: Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing.
Authors: Watson, W.T. / Minogue, T.D. / Val, D.L. / von Bodman, S.B. / Churchill, M.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Rhenium MAD Phasing of the Acyl-homoserinelactone Synthase EsaI
Authors: Watson, W.T. / Murphy IV, F.V. / Gould, T.A. / Jambeck, P. / Val, D.L. / Cronan JR., J.E. / Beck von Bodman, S. / Churchill, M.E.A.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acyl-homoserinelactone synthase EsaI


Theoretical massNumber of molelcules
Total (without water)26,0411
Polymers26,0411
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.991, 66.991, 47.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein acyl-homoserinelactone synthase EsaI


Mass: 26040.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea stewartii subsp. stewartii (bacteria)
Species: Pantoea stewartii / Strain: subsp. stewartii / Gene: EsaI/EsaR gene cluster / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54656
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: MES, PEG 4000, 2-propanol, EDTA, NaN3, 2-mercaptoethanol, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
20.1 MMES1reservoirpH6.1
314 %PEG40001reservoir
46 %isopropanol1reservoir
50.03 %beta-mercaptoethanol1reservoir
610 mMEDTA1reservoir
70.5 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2000
RadiationMonochromator: CARS-designed Si(111) double-bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. all: 19521 / Num. obs: 19521 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 28.553 Å2 / Rsym value: 0.039 / Net I/σ(I): 48.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 1799 / Rsym value: 0.195 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 174794 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.195

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4J

1k4j


Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1851 -random
Rwork0.2087 ---
all0.224 18828 --
obs0.224 18828 96.6 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2---1.89 Å20 Å2
3---3.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-30 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 100 1649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00917
X-RAY DIFFRACTIONc_angle_d1.349
X-RAY DIFFRACTIONc_dihedral_angle_d23.48
X-RAY DIFFRACTIONc_improper_angle_d0.957
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.289 299 -
Rwork0.24 --
obs-3033 0.941 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 9.5 % / Rfactor all: 0.224 / Rfactor obs: 0.209 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0092
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.48
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.957
LS refinement shell
*PLUS
Lowest resolution: 1.86 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.251 / Rfactor obs: 0.251

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