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- PDB-6gpd: Crystal structure of the ligand-free form of domain 1 from TmArgBP -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gpd | ||||||
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Title | Crystal structure of the ligand-free form of domain 1 from TmArgBP | ||||||
![]() | Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Smaldone, G. / Balasco, N. / Ruggiero, A. / Berisio, R. / Vitagliano, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.9 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gpcC ![]() 6gpmC ![]() 4prsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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