+Open data
-Basic information
Entry | Database: PDB / ID: 3ip9 | |||||||||
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Title | Structure of Atu2422-GABA receptor in complex with GABA | |||||||||
Components | ABC transporter, substrate binding protein (Amino acid) | |||||||||
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: 1.8 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 | 3ip9.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ip9.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ip9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ip9 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ip9 | HTTPS FTP |
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-Related structure data
Related structure data | 3ip5SC 3ip6SC 3ip7SC 3ipaC 3ipcC 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
#1: Protein | Mass: 37514.070 Da / Num. of mol.: 1 / Fragment: UNP residues 24-372 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-ABU / |
#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: 42.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, 6.5% 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: May 14, 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: 1.8→32.388 Å / Num. all: 29021 / Num. obs: 29021 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.097 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.7 % / Num. unique all: 4526 / Rsym value: 0.51 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 3IP5,3IP6,3IP7 Resolution: 1.8→32.388 Å / SU ML: 1.39 / 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: 42.141 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→32.388 Å
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Refine LS restraints |
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LS refinement shell |
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