+Open data
-Basic information
Entry | Database: PDB / ID: 3lrb | |||||||||
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Title | Structure of E. coli AdiC | |||||||||
Components | Arginine/agmatine antiporter | |||||||||
Keywords | TRANSPORT PROTEIN / transporter / antiporter / AdiC / Amino-acid transport / Antiport / Cell inner membrane / Cell membrane / Membrane / Transmembrane / Transport | |||||||||
Function / homology | : / Amino acid/polyamine transporter I / Amino acid permease / antiporter activity / amino acid transport / identical protein binding / plasma membrane / Arginine/agmatine antiporter Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.61 Å | |||||||||
Authors | Gao, X. / Lu, F. / Zhou, L. / Shi, Y. | |||||||||
Citation | Journal: Science / Year: 2009 Title: Structure and mechanism of an amino acid antiporter Authors: Gao, X. / Lu, F. / Zhou, L. / Dang, S. / Sun, L. / Li, X. / Wang, J. / Shi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lrb.cif.gz | 321.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lrb.ent.gz | 267.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lrb_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 3lrb_full_validation.pdf.gz | 546.4 KB | Display | |
Data in XML | 3lrb_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 3lrb_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrb ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 46869.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: adiC, Z5717, ECs5097 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60063 |
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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: 3.7 Å3/Da / Density % sol: 66.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.4% NG, 0.1mM Tris, 22% (w/v) PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K , temperature 291.0K |
-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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.61→50 Å / Num. obs: 16598 / Redundancy: 10.8 % / Biso Wilson estimate: 152.36 Å2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 3.61→3.75 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.463 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.61→49.323 Å / SU ML: 0.58 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 36.94 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.273 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 188.562 Å2
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Refinement step | Cycle: LAST / Resolution: 3.61→49.323 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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