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Yorodumi- PDB-2uyf: Single mutant F111L DntR from Burkholderia sp. strain DNT in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uyf | ||||||
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Title | Single mutant F111L DntR from Burkholderia sp. strain DNT in complex with thiocyanate | ||||||
Components | REGULATORY PROTEIN | ||||||
Keywords | TRANSCRIPTION / LTTR / LYSR / DNA-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTIONAL REGULATOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA CEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lonneborg, R. / Smirova, I. / Dian, C. / Leonard, G.A. / Mcsweeney, S. / Brzezinski, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: In Vivo and in Vitro Investigation of Transcriptional Regulation by Dntr. Authors: Lonneborg, R. / Smirova, I. / Dian, C. / Leonard, G.A. / Brzezinski, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uyf.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uyf.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 2uyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyf ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyf | HTTPS FTP |
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-Related structure data
Related structure data | 2uyeC 1uthS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.53179, -0.82093, 0.20804), Vector: |
-Components
#1: Protein | Mass: 34681.074 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: STRAIN DNT / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4 / References: UniProt: Q8VUD7 #2: Chemical | ChemComp-SCN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 4.67 Å3/Da / Density % sol: 73.44 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M IMIDAZOL PH 6.5 0.2M KSCN 1.2M NA ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 51204 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Biso Wilson estimate: 39.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UTH Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.843 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A88 AND B1-B75 ARE DISORDERED. ATOMS BGLN A 292 CG (78.479, 7.234, 105.723, 32.55), CD (77.505, 7.365, 106.893, 34.27), OE1 (77. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A88 AND B1-B75 ARE DISORDERED. ATOMS BGLN A 292 CG (78.479, 7.234, 105.723, 32.55), CD (77.505, 7.365, 106.893, 34.27), OE1 (77.015, 6.365, 107.423, 32.48), NE2 (77.234, 8.597, 107.299, 33.25) HAVE 0.00 OCCUPANCY
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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: 35.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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