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Yorodumi- PDB-2uye: Double mutant Y110S,F111V DntR from Burkholderia sp. strain DNT i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uye | ||||||
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Title | Double mutant Y110S,F111V 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 | 2uye.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uye.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 2uye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uye ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uye | HTTPS FTP |
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-Related structure data
Related structure data | 2uyfC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.52347, -0.82519, 0.21222), Vector: |
-Components
#1: Protein | Mass: 34590.949 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: DNT / Plasmid: PQE60 / Cell line (production host): M15/PREP4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8VUD7 #2: Chemical | ChemComp-SCN / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 110 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 111 TO VAL ...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: 4.7 Å3/Da / Density % sol: 73.61 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M IMIDAZOL PH 6.5 0.2M KSCN 0.9M 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→67.57 Å / Num. obs: 50378 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Biso Wilson estimate: 43.38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UTH Resolution: 2.2→67.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.072 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A87, B1-B75 AND B135 ARE DISORDERED. ATOMS BARG A 168 CZ (94.774, 6.083, 89.947, 56.8), NH1 (95.971, 6.608, 90.140, 57.53), NH2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A87, B1-B75 AND B135 ARE DISORDERED. ATOMS BARG A 168 CZ (94.774, 6.083, 89.947, 56.8), NH1 (95.971, 6.608, 90.140, 57.53), NH2 (94.651, 4.778, 89.771, 57.73) 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: 39.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→67.57 Å
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Refine LS restraints |
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