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Yorodumi- PDB-6f2w: Bacterial asc transporter crystal structure in open to in conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f2w | ||||||
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Title | Bacterial asc transporter crystal structure in open to in conformation | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / LeuT fold / LAT transporter / APC transporter | ||||||
Function / homology | Amino acid/polyamine transporter I / Amino acid permease / transmembrane transporter activity / membrane / ALPHA-AMINOISOBUTYRIC ACID / Putative amino acid/polyamine transport protein Function and homology information | ||||||
Biological species | Carnobacterium sp. AT7 (bacteria) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Fort, J. / Errasti-Murugarren, E. / Carpena, X. / Palacin, M. / Fita, I. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction. Authors: Errasti-Murugarren, E. / Fort, J. / Bartoccioni, P. / Diaz, L. / Pardon, E. / Carpena, X. / Espino-Guarch, M. / Zorzano, A. / Ziegler, C. / Steyaert, J. / Fernandez-Recio, J. / Fita, I. / Palacin, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f2w.cif.gz | 232.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f2w.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 6f2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f2w_validation.pdf.gz | 681.9 KB | Display | wwPDB validaton report |
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Full document | 6f2w_full_validation.pdf.gz | 695.2 KB | Display | |
Data in XML | 6f2w_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 6f2w_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f2w ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f2w | HTTPS FTP |
-Related structure data
Related structure data | 6f2gSC 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: 47597.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carnobacterium sp. AT7 (bacteria) / Gene: CAT7_03719 / Plasmid: pTTQ18 / Details (production host): C-ter 3C site and GFP-His6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A8UCQ5 |
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#2: Antibody | Mass: 14422.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Details (production host): phage display vector / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 (Su) |
#3: Chemical | ChemComp-AIB / |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.08 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 28%PEG400 0,1M 0,1M Ammonium acetate pH8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→66.9 Å / Num. obs: 17358 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.105 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 849 / CC1/2: 0.363 / Rpim(I) all: 0.454 / Rrim(I) all: 1.247 / % possible all: 99.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F2G Resolution: 3.4→24.96 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.891 / SU B: 76.972 / SU ML: 0.489 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Final anisotropy correction with the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/ ref. M. Strong, M.R. Sawaya, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Final anisotropy correction with the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/ ref. M. Strong, M.R. Sawaya, S. Wang, M. Phillips, D. Cascio, D. Eisenberg, Proc Natl Acad Sci USA. 103, 8060-8-65, 2006).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 139.545 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→24.96 Å
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Refine LS restraints |
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