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Open data
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Basic information
Entry | Database: PDB / ID: 5dxz | ||||||
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Title | Crystal of AmtR from Corynebacterium glutamicum | ||||||
![]() | TetR family transcriptional regulator | ||||||
![]() | 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 / 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 | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 439.4 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dy0C ![]() 5dy1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26965.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: KIQ_008455 / Plasmid: pLIC-SGC1 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | Strain used is ATCC 13969. The only difference with the ATCC 14067 is the change of Val141 to Ile. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium Sulphate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.25→36.69 Å / Num. obs: 12703 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Net I/σ(I): 22.5 / Num. measured all: 139352 / Scaling rejects: 81 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DY1 Resolution: 2.25→36.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2496 / WRfactor Rwork: 0.2259 / FOM work R set: 0.8168 / SU B: 13.446 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2656 / SU Rfree: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.54 Å2 / Biso mean: 44.905 Å2 / Biso min: 24.2 Å2
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Refinement step | Cycle: final / Resolution: 2.25→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.309 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 36.755 Å / Origin y: -4.019 Å / Origin z: -19.107 Å
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