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Yorodumi- PDB-2y7k: DntR Inducer Binding Domain in Complex with Salicylate. Monoclini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y7k | ||||||
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Title | DntR Inducer Binding Domain in Complex with Salicylate. Monoclinic crystal form | ||||||
Components | LYSR-TYPE REGULATORY PROTEIN | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / LYSR TYPE / TRANSCRIPTION REGULATOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA SP. DNT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Devesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2011 Title: Crystal Structures of Dntr Inducer Binding Domains in Complex with Salicylate Offer Insights Into the Activation of Lysr-Type Transcriptional Regulators. Authors: Devesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y7k.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y7k.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y7k_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 2y7k_full_validation.pdf.gz | 482.7 KB | Display | |
Data in XML | 2y7k_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 2y7k_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y7k ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y7k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24851.852 Da / Num. of mol.: 4 / Fragment: INDUCER-BINDING DOMAIN, RESIDUES 90-301 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA SP. DNT (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50 #2: Chemical | ChemComp-SAL / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 90 TO MET ENGINEERED RESIDUE IN CHAIN B, PHE 90 TO MET ...ENGINEERED | Sequence details | SEQUENCE CRYSTALLIZ | |
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Details: 31% PEG 8000, 0.1 M TRIS HCL PH 8.0, AND 0.2 M NA/K TARTRATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→82.1 Å / Num. obs: 65440 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.265 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.249 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
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Refine LS restraints |
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