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Yorodumi- PDB-4c0e: Structure of the NOT1 superfamily homology domain from Chaetomium... -
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-Basic information
Entry | Database: PDB / ID: 4c0e | ||||||
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Title | Structure of the NOT1 superfamily homology domain from Chaetomium thermophilum | ||||||
Components | NOT1NotI | ||||||
Keywords | GENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CHAETOMIUM THERMOPHILUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Chen, Y. / Boland, A. / Raisch, T. / Jonas, S. / Izaurralde, E. / Weichenrieder, O. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structure and Assembly of the not Module of the Human Ccr4-not Complex Authors: Boland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Kuzuoglu-Ozturk, D. / Wohlbold, L. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c0e.cif.gz | 769.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c0e.ent.gz | 665.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c0e ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c0e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 59983.105 Da / Num. of mol.: 4 Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1676-2193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G0SAL9 Sequence details | THE TEN N-TERMINAL RESIDUES REMAIN FROM THE INCOMPLETE | |
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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: 2.8 Å3/Da / Density % sol: 56 % Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97925 A, PEAK DATA AT THE SE EDGE IN SG19. |
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Crystal grow | pH: 6 Details: 100MM MES PH=6.0, 180MM MGCL2, 5% PEG20000, 10MM PROLINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→90.9 Å / Num. obs: 41851 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 76.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.2→63.61 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 27.74 / Stereochemistry target values: ML Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1674, 1682, 1715, 1801, 1802, 1804, 1867, 1880, 1981, 1996, 2001, 2005, 2031, 2035, 2133, 2141, 2142, ...Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1674, 1682, 1715, 1801, 1802, 1804, 1867, 1880, 1981, 1996, 2001, 2005, 2031, 2035, 2133, 2141, 2142, 2163, 2170, 2174, 2175, 2178, 2181. CHAIN B, RESIDUES 1673, 1682, 1715, 1750, 1801, 1802, 1804, 1880, 1960, 1962, 1973, 1976, 1981, 1982, 2001, 2004, 2005, 2013, 2021, 2026, 2032, 2035, 2036, 2038, 2062, 2064, 2070, 2077, 2123, 2125, 2128, 2163, 2170, 2171, 2175, 2191. CHAIN C, RESIDUES 1666, 1696, 1700, 1701, 1702, 1720, 1721, 1722, 1737, 1770, 1772, 1831, 1867, 1880, 1960, 1963, 1973, 1976, 1982, 2001, 2005, 2013, 2014, 2025, 2027, 2038, 2123, 2128, 2145, 2172, 2174, 2175, 2176, 2178, 2183, 2186, 2190, 2191. CHAIN D, RESIDUES 1670, 1696, 1700, 1701, 1720, 1721, 1722, 1770, 1772, 1774, 1775, 1867, 1880, 1969, 1973, 1975, 1976, 1981, 1983, 1996, 2001, 2009, 2013, 2025, 2026, 2035, 2038, 2055, 2062, 2064, 2066, 2123, 2124, 2128, 2130, 2133, 2138, 2141, 2145, 2163, 2168, 2170, 2171, 2172, 2175, 2176, 2178, 2180, 2183, 2190. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1771 TO 1777, 2027 TO 2030. CHAIN B, RESIDUES 1770 TO 1777, 2027 TO 2031, 2092, 2093. CHAIN C, RESIDUES 1774 TO 1776, 2028 TO 2033, 2092, 2093. CHAIN D, RESIDUES 1776, 2027 TO 2033, 2091 TO 2093.
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.352 Å2 / ksol: 0.326 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.6 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→63.61 Å
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Refine LS restraints |
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LS refinement shell |
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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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