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- PDB-2ixg: Crystal structure of the ATPase domain of TAP1 with ATP (S621A, G... -
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Basic information
Entry | Database: PDB / ID: 2ixg | ||||||
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Title | Crystal structure of the ATPase domain of TAP1 with ATP (S621A, G622V, D645N mutant) | ||||||
![]() | ANTIGEN PEPTIDE TRANSPORTER 1 | ||||||
![]() | HYDROLASE / ENDOPLASMIC RETICULUM / MEMBRANE / TRANSPORT / ABC ATPASE / ATP- BINDING / PROTEIN TRANSPORT / NUCLEOTIDE-BINDING / TRANSMEMBRANE / IMMUNE RESPONSE / PEPTIDE TRANSPORT | ||||||
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 | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.5 KB | Display | ![]() |
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Full document | ![]() | 761.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ixeSC ![]() 2ixfC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29508.521 Da / Num. of mol.: 1 / 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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 621 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLY 622 TO VAL ...ENGINEERED |
Sequence details | RESIDUE 464 IS THE START METHIONINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: SITTING DROP VAPOR DIFFUSION WITH A RESERVOIR CONTAINING 1.5 M SODIUM MALONATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 11, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 7168 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IXE Resolution: 2.7→26.47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.885 / SU B: 28.66 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→26.47 Å
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Refine LS restraints |
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