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Yorodumi- PDB-5eue: S1P Lyase Bacterial Surrogate bound to N-(2-((4-methoxy-2,5-dimet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eue | ||||||
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Title | S1P Lyase Bacterial Surrogate bound to N-(2-((4-methoxy-2,5-dimethylbenzyl)amino)-1-phenylethyl)-5-methylisoxazole-3-carboxamide | ||||||
Components | Putative sphingosine-1-phosphate lyase | ||||||
Keywords | LYASE / S1P Lyase bacterial surrogate | ||||||
Function / homology | Function and homology information sphinganine-1-phosphate aldolase activity / aromatic-L-amino-acid decarboxylase activity / aspartate 1-decarboxylase activity / sphingolipid catabolic process / carboxylic acid metabolic process / coenzyme A biosynthetic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Symbiobacterium thermophilum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Argiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. ...Argiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. / Wallace, G. / Harris, C.M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2016 Title: Creation of a S1P Lyase bacterial surrogate for structure-based drug design. Authors: Argiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. / Wallace, G. / Harris, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eue.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eue.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 5eue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eue ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eue | HTTPS FTP |
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-Related structure data
Related structure data | 5eudC 3madS C: citing same article (ref.) S: Starting model for refinement |
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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: 55741.043 Da / Num. of mol.: 2 / Mutation: Y249F, L344I, F346A, L497S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Symbiobacterium thermophilum (strain T / IAM 14863) (bacteria) Strain: T / IAM 14863 / Gene: STH1274 / Production host: Escherichia coli (E. coli) / References: UniProt: Q67PY4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.15 M KCSN, 0.1M Tris, pH 8.3, 18% PEG 5000 MME / PH range: 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→129.6 Å / Num. obs: 22823 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 61.86 Å2 / Rsym value: 0.11 / Net I/σ(I): 15.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MAD Resolution: 2.83→71.09 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.8725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.387
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Displacement parameters | Biso mean: 46.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.288 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→71.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.83→2.97 Å / Total num. of bins used: 11
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