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Yorodumi- PDB-3g40: Crystal structure of the cytoplasmic domain of a prokaryotic cati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g40 | ||||||
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Title | Crystal structure of the cytoplasmic domain of a prokaryotic cation chloride cotransporter | ||||||
Components | Na-K-Cl cotransporter | ||||||
Keywords | TRANSPORT PROTEIN / alpha/beta fold 10-stranded twisted beta sheet | ||||||
Function / homology | Amino acid permease/ SLC12A domain / Amino acid permease / transmembrane transport / membrane => GO:0016020 / identical protein binding / Na-K-Cl cotransporter Function and homology information | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Warmuth, S. / Zimmermann, I. / Dutzler, R. | ||||||
Citation | Journal: Structure / Year: 2009 Title: X-ray Structure of the C-Terminal Domain of a Prokaryotic Cation-Chloride Cotransporter Authors: Warmuth, S. / Zimmermann, I. / Dutzler, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g40.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g40.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g40 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g40 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33244.980 Da / Num. of mol.: 1 / Fragment: MaCCC C-terminal domain, UNP residues 492-758' Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA4506 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8THK8 |
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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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 1.1M MgSO4, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.964 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2006 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 29560 / Num. obs: 28259 / % possible obs: 95.6 % / Observed criterion σ(F): 6.39 / Observed criterion σ(I): 6.39 / Redundancy: 6.6 % / Rsym value: 0.066 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1087 / Rsym value: 0.383 / % possible all: 74.6 |
-Processing
Software |
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Refinement | Resolution: 1.9→9.907 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / SU ML: 0.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.229 Å2 / ksol: 0.421 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 264.03 Å2 / Biso mean: 55.693 Å2 / Biso min: 25.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→9.907 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Details: all / Origin x: -4.8183 Å / Origin y: 41.9711 Å / Origin z: 45.7529 Å
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Refinement TLS group | Selection details: chain A 19-287 |