+Open data
-Basic information
Entry | Database: PDB / ID: 4dji | ||||||
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Title | Structure of glutamate-GABA antiporter GadC | ||||||
Components | Probable glutamate/gamma-aminobutyrate antiporter | ||||||
Keywords | TRANSPORT PROTEIN / LeuT fold / glutamate-GABA antiporter | ||||||
Function / homology | Glutamate:g-aminobutyrate antiporter / Amino acid/polyamine transporter I / Amino acid permease / intracellular pH elevation / antiporter activity / amino acid transport / plasma membrane / Glutamate/gamma-aminobutyrate antiporter Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.187 Å | ||||||
Authors | Ma, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure and mechanism of a glutamate-GABA antiporter Authors: Ma, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dji.cif.gz | 376.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dji.ent.gz | 314.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dji_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 4dji_full_validation.pdf.gz | 606.7 KB | Display | |
Data in XML | 4dji_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 4dji_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/4dji ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4dji | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 55114.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gadC / Production host: Escherichia coli (E. coli) / References: UniProt: P63235 |
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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: 3.5 Å3/Da / Density % sol: 64.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG400, 100mM Tris-HCl, 200mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 11, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.187→40 Å / Num. all: 26653 / Num. obs: 22522 / % possible obs: 84.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 89.21 Å2 |
Reflection shell | Resolution: 3.187→3.31 Å / % possible all: 47 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.187→35.518 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6955 / SU ML: 0.99 / σ(F): 1.35 / Phase error: 35.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.768 Å2 / ksol: 0.284 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 257.79 Å2 / Biso mean: 108.5685 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.187→35.518 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: 8
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Refinement TLS params. | Method: refined / Origin x: -29.5593 Å / Origin y: -4.2023 Å / Origin z: 22.0175 Å
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Refinement TLS group |
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