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Yorodumi- PDB-4kvf: The crystal structure of a rhamnose ABC transporter, periplasmic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kvf | ||||||
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Title | The crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836 | ||||||
Components | Rhamnose ABC transporter, periplasmic rhamnose-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information rhamnose transmembrane transport / ATP-binding cassette (ABC) transporter complex Similarity search - Function | ||||||
Biological species | Kribbella flavida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.722 Å | ||||||
Authors | Tan, K. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836 Authors: Tan, K. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kvf.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kvf.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 4kvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/4kvf ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kvf | 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 on special symmetry positions |
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Details | Experimentally unknown. It is predicted to be a monomer. |
-Components
#1: Protein | Mass: 35689.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_0259 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2PT67 | ||
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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: 1.81 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.01M sodium citrate, 33% (w/v) PEG6000, pH 7.0, 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: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→27.5 Å / Num. all: 30087 / Num. obs: 30087 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1476 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.722→27.17 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.722→27.17 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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