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Yorodumi- PDB-3ipc: Structure of ATU2422-GABA F77A mutant receptor in complex with leucine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ipc | ||||||
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Title | Structure of ATU2422-GABA F77A mutant receptor in complex with leucine | ||||||
Components | ABC transporter, substrate binding protein (Amino acid)ATP-binding cassette transporter | ||||||
Keywords | TRANSPORT PROTEIN / VENUS FLYTRAP DOMAIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Morera, S. / Planamente, S. / Vigouroux, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: A conserved mechanism of GABA binding and antagonism is revealed by structure-function analysis of the periplasmic binding protein Atu2422 in Agrobacterium tumefaciens. Authors: Planamente, S. / Vigouroux, A. / Mondy, S. / Nicaise, M. / Faure, D. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ipc.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ipc.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ipc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ipc ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ipc | HTTPS FTP |
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-Related structure data
Related structure data | 3ip5SC 3ip6SC 3ip7SC 3ip9SC 3ipaSC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37437.977 Da / Num. of mol.: 1 / Fragment: UNP residues 24-372 / Mutation: F77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4394, Atu2422 / Plasmid: pET-9aSN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: Q7CX36 |
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#2: Chemical | ChemComp-LEU / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, 6% glycerol, 2.5 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2009 / Details: kirkpatrick baez |
Radiation | Monochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→32.1 Å / Num. all: 68599 / Num. obs: 68599 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.3→1.39 Å / Redundancy: 1.8 % / Num. unique all: 6206 / Rsym value: 0.337 / % possible all: 50 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 3IP5,3IP6,3IP7,3IP9,3IPA Resolution: 1.3→32.1 Å / SU ML: 0.02 / σ(F): 1.99 / 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: 47.231 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→32.1 Å
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Refine LS restraints |
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LS refinement shell |
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