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Yorodumi- PDB-4dgf: Structure of SulP Transporter STAS Domain from Wolinella Succinog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dgf | ||||||
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Title | Structure of SulP Transporter STAS Domain from Wolinella Succinogenes Refined to 1.6 Angstrom Resolution | ||||||
Components | SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / STAS Domain / Anion Exchange / Membrane / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information inorganic anion transmembrane transport / monoatomic anion transmembrane transporter activity / membrane Similarity search - Function | ||||||
Biological species | Wolinella succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Keller, J.P. / Chang, C. / Tesar, C. / Bearden, J. / Dallos, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of SulP Transporter STAS Domain from Wolinella Succinogenes Refined to 1.6 Angstrom Resolution Authors: Keller, J.P. / Chang, C. / Dallos, P. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dgf.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dgf.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/4dgf ftp://data.pdbj.org/pub/pdb/validation_reports/dg/4dgf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15217.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: YCHM, WS0651 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M9V0 #2: Chemical | #3: Chemical | #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 Matthews: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 60% Tacsimate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. all: 38860 / Num. obs: 38860 / % possible obs: 99.8 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Redundancy: 12.3 % |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5494 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→59.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.301 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): -1000 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→59.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.597→1.639 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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