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Yorodumi- PDB-3apu: Crystal structure of the A variant of human alpha1-acid glycoprotein -
+Open data
-Basic information
Entry | Database: PDB / ID: 3apu | ||||||
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Title | Crystal structure of the A variant of human alpha1-acid glycoprotein | ||||||
Components | Alpha-1-acid glycoprotein 2Orosomucoid | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / PLASMA PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / azurophil granule lumen / positive regulation of tumor necrosis factor production / Platelet degranulation / collagen-containing extracellular matrix ...positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / azurophil granule lumen / positive regulation of tumor necrosis factor production / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nishi, K. / Ono, T. / Nakamura, T. / Fukunaga, N. / Izumi, M. / Watanabe, H. / Suenaga, A. / Maruyama, T. / Yamagata, Y. / Curry, S. / Otagiri, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2011 Title: Structural insights into differences in drug-binding selectivity between two forms of human alpha1-acid glycoprotein genetic variants, the A and F1*S forms. Authors: Nishi, K. / Ono, T. / Nakamura, T. / Fukunaga, N. / Izumi, M. / Watanabe, H. / Suenaga, A. / Maruyama, T. / Yamagata, Y. / Curry, S. / Otagiri, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3apu.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3apu.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 3apu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3apu ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3apu | HTTPS FTP |
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-Related structure data
Related structure data | 3apvC 3apwC 3apxC 3bx6 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22691.287 Da / Num. of mol.: 2 / Mutation: C149R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGP2, ORM2 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19652 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 38.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 21258 / Num. obs: 21258 / % possible obs: 99.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 56.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 6.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BX6 3bx6 Resolution: 2.1→31.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 14.626 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.191 / 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: 51.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→31.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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