+Open data
-Basic information
Entry | Database: PDB / ID: 3ip5 | ||||||
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Title | Structure of Atu2422-GABA receptor in complex with alanine | ||||||
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: 1.35 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 | 3ip5.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ip5.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ip5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/3ip5 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/3ip5 | HTTPS FTP |
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-Related structure data
Related structure data | 3ip6C 3ip7C 3ip9C 3ipaC 3ipcC 1uskS 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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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-ALA / |
#3: Chemical | ChemComp-PEG / |
#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: 42.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 35% PEG 4000, 100 mM CACL2, 0.1 M Tris-HCl, 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: Jul 16, 2008 / 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: 1.35→30 Å / Num. all: 69760 / Num. obs: 69760 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.104 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 4 % / Num. unique all: 9671 / Rsym value: 0.509 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1USK Resolution: 1.35→30 Å / SU ML: 0.14 / 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: 53.965 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
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Refine LS restraints |
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LS refinement shell |
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