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- PDB-7e4j: X-ray crystal structure of VapB12 antitoxin from mycobacterium tu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e4j | ||||||
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Title | X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41. | ||||||
![]() | Antitoxin | ||||||
![]() | ANTITOXIN / VapBC12 / Toxin-antitoxin / Cholesterol | ||||||
Function / homology | Ribbon-helix-helix / regulation of DNA-templated transcription / Antitoxin![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pratap, S. / Megta, A.K. / Talwar, S. / Chandresh, S. / Pandey, A.K. / Krishnan, V. | ||||||
![]() | ![]() Title: X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41. Authors: Pratap, S. / Megta, A.K. / Talwar, S. / Sharma, C. / Pandey, A.K. / Krishnan, 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 | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.5 KB | Display | ![]() |
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Full document | ![]() | 416.5 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 44 / Label seq-ID: 1 - 44
NCS ensembles :
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Components
#1: Protein/peptide | Mass: 4941.749 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_ ...Gene: vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_02694, ERS027646_03040, ERS027659_01239, ERS027661_00782, ERS094182_03044, F6W99_00284, FRD82_02990, SAMEA2683035_01359 Production host: ![]() ![]() References: UniProt: A0A045KH53 #2: Chemical | ChemComp-ZN / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.3 Details: 0.2 M Ammonium Chloride:NaOH pH 6.3, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.63→40.56 Å / Num. obs: 23505 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.6 | |||||||||||||||
Reflection shell | Resolution: 1.635→1.663 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / Num. unique obs: 1174 / CC1/2: 0.806 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.63→40.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.816 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.02 / 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: 38.852 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→40.56 Å
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Refine LS restraints |
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