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Yorodumi- PDB-3gi8: Crystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gi8 | ||||||
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Title | Crystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclonal Fab Fragment | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / membrane protein / transporter / antibody / 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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 | 3gi8.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gi8.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gi8 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gi8 | HTTPS FTP |
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-Related 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: 48272.117 Da / Num. of mol.: 1 / Mutation: K158A 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: Antibody | Mass: 24284.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Murine Hybridoma / Production host: Mus musculus (house mouse) |
#3: Antibody | Mass: 23984.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Murine Hybridoma / Production host: Mus musculus (house mouse) |
#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: 3.07 Å3/Da / Density % sol: 59.89 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5 Details: 0.1M sodium acetate, 0.1M ammonium dihydrogen phosphate, 40-44% PEG 400, pH 5.0, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2008 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal/Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 36142 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ApcT - Fab complex Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.891 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.364 / 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: 56.772 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.658 Å / Total num. of bins used: 20
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