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Yorodumi- PDB-6ggp: Structure of the ligand-free form of truncated ArgBP (residues 20... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ggp | ||||||
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Title | Structure of the ligand-free form of truncated ArgBP (residues 20-233) 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 | 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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 | 6ggp.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggp.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ggp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggp ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggp | HTTPS FTP |
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-Related structure data
Related structure data | 6ggvC 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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Unit cell |
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-Components
#1: Protein | Mass: 23443.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystals grew in 16-20 mg/mL protein solution and in 30 % w/v PEG 8,000, 0.1 M Sodium cacodylate trihydrate (pH 6.5) and 0.2 M Sodium Acetate trihydrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9464 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: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→20 Å / Num. obs: 104443 / % possible obs: 95.9 % / Redundancy: 13.7 % / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.03→1.05 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PRS Resolution: 1.03→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.594 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.027 / 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: 8.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.03→15 Å
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Refine LS restraints |
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