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Yorodumi- PDB-3d3o: Crystal structure of the effector domain of the putative transcri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d3o | ||||||
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Title | Crystal structure of the effector domain of the putative transcriptional regulator IclR from Acinetobacter sp. ADP1 | ||||||
Components | Putative transcriptional regulator, IcIR family | ||||||
Keywords | TRANSCRIPTION REGULATOR / alpha-beta structure / effector domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å | ||||||
Authors | Kim, Y. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Effector Domain of the Putative Transcriptional Regulator IclR from Acinetobacter sp. ADP1. Authors: Kim, Y. / Shackelford, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d3o.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d3o.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 3d3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d3o_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 3d3o_full_validation.pdf.gz | 461 KB | Display | |
Data in XML | 3d3o_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3d3o_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3o ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3o | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 20524.051 Da / Num. of mol.: 2 / Fragment: Effector domain: Residues 81-255 Source method: isolated from a genetically manipulated source Details: N-term 6-His-tag with TEV protease cleavage site / Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: ACIAD1822 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FBA6 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NH4 / | #4: 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: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 1.26M Ammonium sulfate, 0.1M CHES pH 9.5, 0.2M NaCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2008 / Details: Mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→35.84 Å / Num. all: 15652 / Num. obs: 15652 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 53.69 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.46→2.5 Å / Redundancy: 9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.3 / Num. unique all: 778 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.46→35.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.088 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.499 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 64.159 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→35.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.524 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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