+Open data
-Basic information
Entry | Database: PDB / ID: 1kzf | ||||||
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Title | Crystal Structure of the Acyl-homoserine Lactone Synthase, EsaI | ||||||
Components | acyl-homoserinelactone synthase EsaI | ||||||
Keywords | LIGASE / 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 | ||||||
Biological species | Pantoea stewartii subsp. stewartii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Watson, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzf.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzf.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kzf_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1kzf_full_validation.pdf.gz | 370.6 KB | Display | |
Data in XML | 1kzf_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1kzf_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzf ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzf | HTTPS FTP |
-Related structure data
Related structure data | 1k4jSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2000 |
Radiation | Monochromator: CARS-designed Si(111) double-bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017
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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
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LS refinement shell | *PLUS Lowest resolution: 1.86 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.251 / Rfactor obs: 0.251 |