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Yorodumi- PDB-3vv5: Crystal structure of TTC0807 complexed with (S)-2-aminoethyl-L-cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vv5 | ||||||
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Title | Crystal structure of TTC0807 complexed with (S)-2-aminoethyl-L-cysteine (AEC) | ||||||
Components | Amino acid ABC transporter, binding protein | ||||||
Keywords | TRANSPORT PROTEIN / AEC-complex / Periplasm substrate binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tomita, T. / Kanemaru, Y. / Hasebe, F. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2013 Title: Two ATP-Binding Cassette Transporters Involved in (S)-2-Aminoethyl-Cysteine Uptake in Thermus thermophilus Authors: Kanemaru, Y. / Hasebe, F. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vv5.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vv5.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/3vv5 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/3vv5 | HTTPS FTP |
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-Related structure data
Related structure data | 3vvdC 3vveC 3vvfC 1lstS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29263.207 Da / Num. of mol.: 2 / Fragment: UNP residues 19-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TTC0807, TT_C0807 / Plasmid: pHIS8-TTC0807 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL / References: UniProt: Q72JG5 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #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: 1.98 Å3/Da / Density % sol: 37.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Sodium sulfate, 20% PEG4000, 10mM AEC, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2010 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.67 Å / Num. all: 37509 / Num. obs: 37509 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LST Resolution: 1.9→30.67 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.45 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.16 / 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: 19.418 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.945 Å / Total num. of bins used: 20
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