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Yorodumi- PDB-2ixf: Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q... -
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-Basic information
Entry | Database: PDB / ID: 2ixf | ||||||
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Title | Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant) | ||||||
Components | ANTIGEN PEPTIDE TRANSPORTER 1 | ||||||
Keywords | HYDROLASE / MEMBRANE / TRANSPORT / ABC PROTEIN TRANSPORT / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport ...tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / TAP1 binding / TAP2 binding / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / ADP binding / defense response / transmembrane transport / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen binding / protein transport / adaptive immune response / nucleotide binding / protein-containing complex binding / endoplasmic reticulum membrane / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Procko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ixf.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ixf.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ixf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixf ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixf | HTTPS FTP |
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-Related structure data
Related structure data | 2ixeSC 2ixgC S: Starting model for refinement 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 domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 470 - 718 / Label seq-ID: 7 - 255
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 29506.486 Da / Num. of mol.: 4 / 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.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36370 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLN 678 TO HIS ...ENGINEERED | Sequence details | RESIDUE 464 IS THE START METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOR DIFFUSION WITH THE RESERVOIR CONTAINING 0.75 M TRI-SODIUM CITRATE PH 8.0 . |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 18, 2006 / 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→40 Å / Num. obs: 74956 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IXE Resolution: 2→38.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.733 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.186 / 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: 29.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.49 Å
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Refine LS restraints |
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