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Yorodumi- PDB-6ggv: Structure of the arginine-bound form of truncated (residues 20-23... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ggv | ||||||
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Title | Structure of the arginine-bound form of truncated (residues 20-233) ArgBP from T. maritima | ||||||
Components | Amino acid ABC transporter, periplasmic amino acid-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Domain swapping / Biosensors / Argininemia diagnosis / Protein structure-stability / Calorimetry | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Smaldone, G. / Berisio, R. / Balasco, N. / D'Auria, S. / Vitagliano, L. / Ruggiero, A. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization. Authors: Smaldone, G. / Berisio, R. / Balasco, N. / D'Auria, S. / Vitagliano, L. / Ruggiero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ggv.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggv.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 6ggv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggv ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggv | HTTPS FTP |
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-Related structure data
Related structure data | 6ggpC 4pshS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23573.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima / Strain: MSB8 / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62 #2: Chemical | #3: Chemical | ChemComp-CD / #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 % sol: 34.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The crystals were obtained using a protein concentration of 16 mg/mL and in 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% (v/v) Polyethylene glycol 400. ...Details: The crystals were obtained using a protein concentration of 16 mg/mL and in 0.1 M Cadmium chloride hydrate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% (v/v) Polyethylene glycol 400. Crystal quality was enhanced in presence of 2.0 M Sodium Thiocyanate or 1.0 M Sodium Bromide. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 9570 / % possible obs: 85.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.6→2.64 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PSH Resolution: 2.69→15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 12.537 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.371 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→15 Å
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Refine LS restraints |
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