+Open data
-Basic information
Entry | Database: PDB / ID: 3gia | ||||||
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Title | Crystal Structure of ApcT Transporter | ||||||
Components | Uncharacterized protein MJ0609 | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / transporter / Cell membrane / Membrane / Transmembrane / Structural Genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Shaffer, P.L. / Goehring, A.S. / Shankaranarayanan, A. / Gouaux, E. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: Science / Year: 2009 Title: Structure and mechanism of a na+-independent amino Acid transporter. Authors: Shaffer, P.L. / Goehring, A. / Shankaranarayanan, A. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gia.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gia.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gia ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gia | HTTPS FTP |
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-Related structure data
Related structure data | 3gi8C 3gi9SC C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48330.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0609 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q58026 | ||||
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#2: Chemical | ChemComp-D10 / #3: Chemical | ChemComp-BCN / | #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: 3.76 Å3/Da / Density % sol: 67.28 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 9 Details: 0.1M Bicine, 0.1M sodium chloride, 39-45% PEG 555 MME, pH 9.0, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2007 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 30472 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.32→2.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GI9 Resolution: 2.32→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.602 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.195 / 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: 38.294 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.383 Å / Total num. of bins used: 20
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