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Yorodumi- PDB-5kbw: Crystal structure of TmRibU, the riboflavin-binding S subunit fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kbw | ||||||||||||||||||
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Title | Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter | ||||||||||||||||||
Components | Riboflavin transporter RibU | ||||||||||||||||||
Keywords | Transport Protein / Membrane Protein / Membrane transport / ECF transporter / vitamins / integral membrane protein | ||||||||||||||||||
Function / homology | Function and homology information riboflavin transport / riboflavin transmembrane transporter activity / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Thermotoga maritima (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6093 Å | ||||||||||||||||||
Authors | Karpowich, N.K. / Wang, D.N. / Song, J.M. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin. Authors: Karpowich, N.K. / Song, J. / Wang, D.N. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kbw.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kbw.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kbw_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5kbw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5kbw_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5kbw_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kbw ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kbw | HTTPS FTP |
-Related structure data
Related structure data | 5kc0SC 5kc4C 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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2 |
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Unit cell |
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Details | Monomer determined by static light scattering |
-Components
#1: Protein | Mass: 19797.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ribU, TM_1455 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1G6 #2: Chemical | #3: 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: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 100mM NaCitrate, pH 5.0, 30% PEG 500 DME, 100mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 10106 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % / Rsym value: 0.08 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.38 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KC0 Resolution: 2.6093→30.483 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2.42 / Phase error: 25.77 / 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: 2.6093→30.483 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.5679 Å / Origin y: -8.8488 Å / Origin z: 76.2462 Å
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Refinement TLS group | Selection details: all |