+Open data
-Basic information
Entry | Database: PDB / ID: 4psh | ||||||
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Title | Structure of holo ArgBP from T. maritima | ||||||
Components | ABC-type transporter, periplasmic subunit family 3 | ||||||
Keywords | PROTEIN TRANSPORT / alpha/beta / arg binding protein | ||||||
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 / ARGININE / Amino acid ABC transporter, periplasmic amino acid-binding protein Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Ruggiero, A. / Dattelbaum, J.D. / Staiano, M. / Berisio, R. / D'Auria, S. / Vitagliano, L. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima Authors: Ruggiero, A. / Dattelbaum, J.D. / Staiano, M. / Berisio, R. / D'Auria, S. / Vitagliano, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4psh.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4psh.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 4psh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4psh ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4psh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25297.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62 #2: Chemical | #3: 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: 3.91 Å3/Da / Density % sol: 68.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M Potassium acetate, 20%(w/v) Polyethylene glycol 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9799 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 30065 / Num. obs: 29302 / % possible obs: 97.46 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.62 Å / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.816 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 30.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.664 Å / Total num. of bins used: 20
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