+Open data
-Basic information
Entry | Database: PDB / ID: 4oye | ||||||
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Title | Crystal structure of GltPh R397A in apo | ||||||
Components | 425aa long hypothetical proton glutamate symport protein | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / alpha-helix / membrane protein | ||||||
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 / Resolution: 4 Å | ||||||
Authors | Boudker, O. / Oh, S. | ||||||
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 | 4oye.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4oye.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 4oye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oye_validation.pdf.gz | 531.2 KB | Display | wwPDB validaton report |
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Full document | 4oye_full_validation.pdf.gz | 641.6 KB | Display | |
Data in XML | 4oye_validation.xml.gz | 159.4 KB | Display | |
Data in CIF | 4oye_validation.cif.gz | 216.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/4oye ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oye | HTTPS FTP |
-Related structure data
Related structure data | 4oyfC 4p19C 4p1aC 4p3jC 4p6hC 5cfyC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 43007.984 Da / Num. of mol.: 12 / Fragment: UNP residues 8-416 Mutation: D37H, K40H, K125H, K132H, K223H, K264H, E368H, R397A 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 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): DH10b / References: UniProt: O59010 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.59 Å3/Da / Density % sol: 73.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG400 Choline chloride citrate/tris |
-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 315r / Detector: CCD / Date: Jul 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 4→20 Å / Num. obs: 52068 / % possible obs: 70.26 % / Redundancy: 2 % / Net I/σ(I): 12.3 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.85 / SU B: 110.309 / SU ML: 0.638 / Cross valid method: THROUGHOUT / ESU R Free: 1.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 137.224 Å2
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Refinement step | Cycle: 1 / Resolution: 4→20 Å
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Refine LS restraints |
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