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Yorodumi- PDB-3u0r: Helical repeat structure of apoptosis inhibitor 5 reveals protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u0r | ||||||
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Title | Helical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules | ||||||
Components | Apoptosis inhibitor 5 | ||||||
Keywords | APOPTOSIS INHIBITOR / HEAT repeat / Armadillo repeat / lysine acetylation | ||||||
Function / homology | Function and homology information negative regulation of fibroblast apoptotic process / fibroblast apoptotic process / fibroblast growth factor binding / spliceosomal complex / nuclear speck / negative regulation of apoptotic process / RNA binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Han, B.G. / Kim, K.H. / Jeong, K.C. / Cho, J.W. / Noh, K.H. / Kim, T.W. / Yoon, H.J. / Suh, S.W. / Lee, S.H. / Lee, B.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Helical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules. Authors: Han, B.G. / Kim, K.H. / Lee, S.J. / Jeong, K.C. / Cho, J.W. / Noh, K.H. / Kim, T.W. / Kim, S.J. / Yoon, H.J. / Suh, S.W. / Lee, S.H. / Lee, B.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u0r.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u0r.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u0r_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 3u0r_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 3u0r_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3u0r_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/3u0r ftp://data.pdbj.org/pub/pdb/validation_reports/u0/3u0r | HTTPS FTP |
-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: 57121.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API5, MIG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZZ5 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE Q9BZZ5 (API5_HUMAN). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10% PEG 6000, 100mM, bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23983, 0.97974, 0.98009, 0.97954, 0.97965 | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2010 | ||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.496→50 Å / Num. all: 19157 / Num. obs: 18250 / Observed criterion σ(F): 0 / Biso Wilson estimate: 43.55 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.123 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 47.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.496→2.561 Å / Total num. of bins used: 20
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