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Yorodumi- PDB-2iks: Crystal structure of N-terminal truncated DNA-binding transcripti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iks | ||||||
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Title | Crystal structure of N-terminal truncated DNA-binding transcriptional dual regulator from Escherichia coli K12 | ||||||
Components | DNA-binding transcriptional dual regulator | ||||||
Keywords | TRANSCRIPTION / DNA-binding transcriptional dual regulator / Escherichia coli K12 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information response to fructose / regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Chang, C. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of N-terminal truncated DNA-binding transcriptional dual regulator from Escherichia coli K12 Authors: Chang, C. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iks.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iks.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 2iks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/2iks ftp://data.pdbj.org/pub/pdb/validation_reports/ik/2iks | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33731.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: GenBank: 1786268, UniProt: P0ACP1*PLUS #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: 2.12 Å3/Da / Density % sol: 41.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 0.3m MgChloride,0.1M Bicine pH8.9, 20% PEG 2K, 1mM fructose 1,6-biphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 48807 / Num. obs: 48758 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 6 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4.47 / Num. unique all: 4811 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.789 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.553 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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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