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Yorodumi- PDB-2yy0: Crystal Structure of MS0802, c-Myc-1 binding protein domain from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yy0 | ||||||
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Title | Crystal Structure of MS0802, c-Myc-1 binding protein domain from Homo sapiens | ||||||
Components | C-Myc-binding protein | ||||||
Keywords | TRANSCRIPTION / conserved hypothetical protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information spermatogenesis / transcription coactivator activity / regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Xie, Y. / Wang, H. / Ihsanawati, K.T. / Kishishita, S. / Takemoto, C. / Shirozu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: crystal structure of c-Myc-1 binding protein domain from Homo sapiens Authors: Xie, Y. / Wang, H. / Ihsanawati, K.T. / Kishishita, S. / Takemoto, C. / Murayama, K. / Shirozu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yy0.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yy0.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 2yy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yy0 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yy0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | in this crystal packing, it looks like dimer. But, there is no experimental evidence. |
-Components
#1: Protein | Mass: 6118.013 Da / Num. of mol.: 4 / Fragment: UNP residues 42-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK060110-05-MD01 / Production host: cell free protein synthesis (others) / References: UniProt: Q99417 #2: 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: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M Tris-HCl, 2M NH4H2PO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2006 / Details: Mirror |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 10097 / Num. obs: 10097 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.02 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 21.63 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 9.83 / Num. unique all: 1444 / Rsym value: 0.265 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→31.11 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1024080.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.9749 Å2 / ksol: 0.397029 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→31.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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