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Yorodumi- PDB-4i6z: Crystal structure of the transcriptional regulator TM1030 with 24... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i6z | ||||||
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Title | Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide | ||||||
Components |
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Keywords | Transcription Regulator/DNA / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / PFAM TetR_N / Helix-turn-helix / TRANSCRIPTIONAL REGULATOR / DNA BINDING / Transcription Regulator-DNA complex | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Koclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide Authors: Koclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6z.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6z.ent.gz | 145.5 KB | Display | PDB format |
PDBx/mmJSON format | 4i6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6z_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 4i6z_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 4i6z_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4i6z_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6z ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6z | HTTPS FTP |
-Related structure data
Related structure data | 2id6S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 200 / Label seq-ID: 3 - 202
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-Components
#1: Protein | Mass: 24409.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM1030, TM_1030 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q9X0C0 #2: DNA chain | Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) synthetic construct (others) #3: 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: 2.69 Å3/Da / Density % sol: 54.21 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion / pH: 8 Details: 0.1M Tris, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 11502 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Χ2: 2.338 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ID6 Resolution: 3.2→33.23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2524 / WRfactor Rwork: 0.1813 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8025 / SU B: 36.056 / SU ML: 0.391 / SU Rfree: 0.5004 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 max: 221.92 Å2 / Biso mean: 82.3858 Å2 / Biso min: 32.46 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→33.23 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10535 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.2→3.283 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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