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Yorodumi- PDB-4kq9: Crystal structure of periplasmic ribose ABC transporter from Cone... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kq9 | ||||||
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Title | Crystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684 | ||||||
Components | Ribose ABC transporter, substrate binding protein | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / ribose binding / PSI-Biology / MCSG / Structural Genomics / Midwest Center for Structural Genomics / ribose transporter | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Ribose ABC transporter, substrate binding protein Function and homology information | ||||||
Biological species | Conexibacter woesei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Nocek, B. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684 Authors: Nocek, B. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kq9.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kq9.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kq9 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kq9 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31667.428 Da / Num. of mol.: 1 / Mutation: V262M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Conexibacter woesei (bacteria) / Strain: DSM 14684 / Gene: Cwoe_4347 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: D3F6W3 | ||
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#2: Chemical | #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: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.1 M DL-Malic Acid, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 27010 / Num. obs: 26570 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→28.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.555 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.156 / ESU R Free: 0.148 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.047 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.906→1.955 Å / Total num. of bins used: 20
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