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Yorodumi- PDB-6gpd: Crystal structure of the ligand-free form of domain 1 from TmArgBP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gpd | ||||||
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Title | Crystal structure of the ligand-free form of domain 1 from TmArgBP | ||||||
Components | Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Domain-domain communication / Diagnostic tool / Protein dissection / Biosensor / Protein structure-stability | ||||||
Function / homology | Bacterial periplasmic substrate-binding proteins / ligand-gated monoatomic ion channel activity / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / membrane / Amino acid ABC transporter, periplasmic amino acid-binding protein Function and homology information | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Smaldone, G. / Balasco, N. / Ruggiero, A. / Berisio, R. / Vitagliano, L. | ||||||
Citation | Journal: Int. J. Biol. Macromol. / Year: 2018 Title: Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection. Authors: Smaldone, G. / Balasco, N. / Vigorita, M. / Ruggiero, A. / Cozzolino, S. / Berisio, R. / Del Vecchio, P. / Graziano, G. / Vitagliano, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gpd.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gpd.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gpd_validation.pdf.gz | 420.9 KB | Display | wwPDB validaton report |
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Full document | 6gpd_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 6gpd_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 6gpd_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gpd ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gpd | HTTPS FTP |
-Related structure data
Related structure data | 6gpcC 6gpmC 4prsS 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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-Components
#1: Protein | Mass: 13857.786 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62 #2: 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: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: The best crystals of D1 domain were obtained using a protein concentration of 6 mg/ml in a solution containing 0.2 M NaCl, 0.1M Bis-Tris (pH 5.5), 25% (w/v) polyethylene glycol (PEG) 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 2015 |
Radiation | Monochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→15 Å / Num. obs: 24812 / % possible obs: 88.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 1.75→1.78 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PRS Resolution: 1.75→14.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.816 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.105 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.293 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→14.4 Å
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Refine LS restraints |
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