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Yorodumi- PDB-3v6a: Helical repeat structure of apoptosis inhibitor 5 reveals protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v6a | ||||||
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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 and Armadillo-like repeat / FGF-2 / Acinus / Nucleus | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lee, B.I. / Han, B.G. / Lee, S.J. | ||||||
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 | 3v6a.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v6a.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 3v6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v6a_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 3v6a_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 3v6a_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3v6a_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/3v6a ftp://data.pdbj.org/pub/pdb/validation_reports/v6/3v6a | HTTPS FTP |
-Related structure data
Related structure data | 3u0rSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53587.355 Da / Num. of mol.: 1 / Fragment: UNP residues 1-454 / Mutation: K251Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API5 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9BZZ5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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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: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 17983 / Num. obs: 17022 / % possible obs: 99.3 % |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U0R Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.687 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.299 / 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: 59.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.599→2.666 Å / Total num. of bins used: 20
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