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- PDB-2ixe: Crystal structure of the ATPase domain of TAP1 with ATP (D645N mutant) -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ixe | ||||||
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Title | Crystal structure of the ATPase domain of TAP1 with ATP (D645N mutant) | ||||||
![]() | ANTIGEN PEPTIDE TRANSPORTER 1 | ||||||
![]() | HYDROLASE / ABC ATPASE | ||||||
Function / homology | ![]() Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / ABC-type oligopeptide transporter activity / peptide transport / peptide transmembrane transporter activity / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / transmembrane transport / ADP binding / defense response / peptide antigen binding / protein transport / adaptive immune response / mitochondrial inner membrane / nucleotide binding / protein-containing complex binding / endoplasmic reticulum membrane / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Procko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R. | ||||||
![]() | ![]() Title: Distinct Structural and Functional Properties of the ATPase Sites in an Asymmetric Abc Transporter. Authors: Procko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.5 KB | Display | ![]() |
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PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ixfC ![]() 2ixgC ![]() 1jj7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99721, -0.01671, 0.07271), Vector: |
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Components
#1: Protein | Mass: 29482.443 Da / Num. of mol.: 2 / Fragment: ATPASE DOMAIN, RESIDUES 465-725 / Mutation: YES Source method: isolated from a genetically manipulated source Details: TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1 (TAP1) Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUE 464 IS THE START METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOR DIFFUSION AT 4C WITH A RESERVOIR CONTAING 1.0 M POTASSIUM PHOSPHATE PH 8.0 |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 38086 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JJ7 Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.288 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.171 / 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: 40.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2→72.55 Å
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Refine LS restraints |
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