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- PDB-5dy0: Crystal of AmtR from Corynebacterium glutamicum in complex with DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dy0 | ||||||
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Title | Crystal of AmtR from Corynebacterium glutamicum in complex with DNA | ||||||
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![]() | DNA BINDING PROTEIN / TetR family regulator / Nitrogen master regulator / PII / GlnK / GlnB / TFR | ||||||
Function / homology | Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / metal ion binding / DNA / DNA (> 10) / TetR family transcriptional regulator![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palanca, C. / Rubio, V. | ||||||
![]() | ![]() Title: Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms. Authors: Palanca, C. / Rubio, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.3 KB | Display | ![]() |
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PDB format | ![]() | 178.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.6 KB | Display | ![]() |
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Full document | ![]() | 495 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dxzC ![]() 5dy1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25477.975 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 7984.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.26 Å3/Da / Density % sol: 80.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 1.2 M Trisodium Citrate, 0.1 M NaHepes pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3→119.94 Å / Num. obs: 67304 / % possible obs: 99 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Net I/σ(I): 17.1 / Num. measured all: 295546 / Scaling rejects: 7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DY1 Resolution: 3→137.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.778 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.257 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.13 Å2
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Refinement step | Cycle: LAST / Resolution: 3→137.42 Å
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Refine LS restraints |
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