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Yorodumi- PDB-3m9x: Open liganded crystal structure of xylose binding protein from Es... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m9x | |||||||||
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Title | Open liganded crystal structure of xylose binding protein from Escherichia coli | |||||||||
Components | D-xylose-binding periplasmic protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / xylose binding protein / xylose / conformational changes | |||||||||
Function / homology | Function and homology information D-xylose transmembrane transport / D-xylose metabolic process / monosaccharide binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / carbohydrate binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Sooriyaarachchi, S. / Ubhayasekera, W. / Mowbray, S.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed Authors: Sooriyaarachchi, S. / Ubhayasekera, W. / Park, C. / Mowbray, S.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m9x.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m9x.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 3m9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m9x_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 3m9x_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 3m9x_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3m9x_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9x ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9x | HTTPS FTP |
-Related structure data
Related structure data | 3m9wSC 3ma0C 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: 34134.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Plasmid: pEXP-5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P37387 |
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#2: Sugar | ChemComp-XYP / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21%(w/v) polyethylene glycol 3350, 0.2M ammonium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 14880 / Rsym value: 0.079 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3M9W Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.795 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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