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Yorodumi- PDB-2e1n: Crystal structure of the Cyanobacterium circadian clock modifier Pex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1n | ||||||
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Title | Crystal structure of the Cyanobacterium circadian clock modifier Pex | ||||||
Components | Pex | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / circadian clock / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Synechococcus elongatus PCC 7942 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Arita, K. / Shimizu, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural and Biochemical Characterization of a Cyanobacterium Circadian Clock-modifier Protein Authors: Arita, K. / Hashimoto, H. / Igari, K. / Akaboshi, M. / Kutsuna, S. / Sato, M. / Shimizu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1n.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1n.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 2e1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1n ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1n | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The structures (Chain A and B) of in the asymmetric unit are biological unit. for a homodimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 16174.178 Da / Num. of mol.: 2 / Fragment: residues 16-148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Species: Synechococcus elongatus / Strain: Pcc 7942 / Gene: pex / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O66226, UniProt: Q31QG0*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.5-1.0M Li2SO4, 0.1M sodium acetate buffer (pH 3.8~4.6), 50mM magnesium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→32.2 Å / Num. all: 24920 / Num. obs: 24505 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.424 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→32.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.32 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.132 / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.343 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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