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Yorodumi- PDB-2iek: New crystal form of transcriptional regulator tm1030 from Thermot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iek | ||||||
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Title | New crystal form of transcriptional regulator tm1030 from Thermotoga maritima | ||||||
Components | Transcriptional regulator, TetR familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTIONAL REGULATOR / TETR FAMILY | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Koclega, K.D. / Chruszcz, M. / Minor, W. | ||||||
Citation | Journal: To be Published Title: New crystal form of transcriptional regulator tm1030 from Thermotoga maritima Authors: Koclega, K.D. / Chruszcz, M. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iek.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iek.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2iek ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2iek | HTTPS FTP |
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-Related structure data
Related structure data | 1zkgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24213.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1030 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q9X0C0 |
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#2: Chemical | ChemComp-P6G / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.05M Na citrate, 30% w/v PEG 2K MME, 0.1M KSCN, 0.01M NH4 sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. all: 17541 / Num. obs: 17541 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.128 / Rsym value: 0.146 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1788 / Rsym value: 0.463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1zkg Resolution: 1.83→19.87 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.167 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Both Refmac and COOT were used in the refinement.
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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: 28.435 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Total num. of bins used: 20
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