+Open data
-Basic information
Entry | Database: PDB / ID: 1j6x | ||||||
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Title | CRYSTAL STRUCTURE OF HELICOBACTER PYLORI LUXS | ||||||
Components | AUTOINDUCER-2 PRODUCTION PROTEIN LUXS | ||||||
Keywords | SIGNALING PROTEIN / alpha-beta fold | ||||||
Function / homology | Function and homology information S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å | ||||||
Authors | Lewis, H.A. / Furlong, E.B. / Bergseid, M.G. / Sanderson, W.E. / Buchanan, S.G. | ||||||
Citation | Journal: Structure / Year: 2001 Title: A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs. Authors: Lewis, H.A. / Furlong, E.B. / Laubert, B. / Eroshkina, G.A. / Batiyenko, Y. / Adams, J.M. / Bergseid, M.G. / Marsh, C.D. / Peat, T.S. / Sanderson, W.E. / Sauder, J.M. / Buchanan, S.G. #1: Journal: Proteins / Year: 2005 Title: Structural analysis of a set of proteins resulting from a bacterial genomics project Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j6x.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j6x.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j6x_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 1j6x_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 1j6x_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1j6x_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/1j6x ftp://data.pdbj.org/pub/pdb/validation_reports/j6/1j6x | HTTPS FTP |
-Related 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: 18704.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZMW8 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: PEG 1000, Ammonium sulfate, MES, BME, NaCl, pH 5.75, VAPOR DIFFUSION, HANGING DROP at 293K, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 5, 2000 | |||||||||
Radiation | Monochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.38→37 Å / Num. all: 13672 / Num. obs: 13672 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 29.9 | |||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.225 / % possible all: 100 | |||||||||
Reflection | *PLUS Rmerge(I) obs: 0.056 | |||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.38→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.38→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.219 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.5 |