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Yorodumi- PDB-4p19: Closed, apo inward-facing state of the glutamate transporter homo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p19 | ||||||
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Title | Closed, apo inward-facing state of the glutamate transporter homologue GltPh | ||||||
Components | 425aa long hypothetical proton glutamate symport protein | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / sodium-coupled aspartate transporter / inward-facing state / apo form | ||||||
Function / homology | Function and homology information amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Verdon, G. / Boudker, O. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2014 Title: Coupled ion binding and structural transitions along the transport cycle of glutamate transporters. Authors: Verdon, G. / Oh, S. / Serio, R.N. / Boudker, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p19.cif.gz | 467.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p19.ent.gz | 392.5 KB | Display | PDB format |
PDBx/mmJSON format | 4p19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/4p19 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/4p19 | HTTPS FTP |
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-Related structure data
Related structure data | 4oyeC 4oyfC 4p1aC 4p3jC 4p6hC 5cfyC 3kbcS 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: 44615.910 Da / Num. of mol.: 3 / Fragment: Residues 1-417 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1295 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): DH10 / References: UniProt: O59010 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: PEG 400, potassium chloride, potassium citrate, magnesium chloride PH range: 5.0 - 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→100 Å / Num. obs: 70319 / % possible obs: 98.7 % / Redundancy: 5.6 % / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3.25→3.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KBC Resolution: 3.25→15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 50.975 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.526 Å2
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Refinement step | Cycle: 1 / Resolution: 3.25→15 Å
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Refine LS restraints |
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