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- PDB-8h2d: The hypothetical protein from Mycobacterium tuberculosis mutant - E47A -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h2d | ||||||
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Title | The hypothetical protein from Mycobacterium tuberculosis mutant - E47A | ||||||
![]() | Uncharacterized protein Rv1546 | ||||||
![]() | HYDROLASE / RNase | ||||||
Function / homology | Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / plasma membrane / Uncharacterized protein Rv1546![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, D.H. / Na, Y. / Lee, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis. Authors: Kim, D.H. / Na, Y. / Chang, H. / Boo, J.H. / Kang, S.M. / Jin, C. / Kang, S.J. / Lee, S.Y. / Lee, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h0hSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15497.699 Da / Num. of mol.: 2 / Mutation: E47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: Rv1546, MTCY48.19c / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris, pH 8.5, 0.2 M ammonium sulfate and 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 6247 / % possible obs: 99.9 % / Redundancy: 12.81 % / Biso Wilson estimate: 87.06 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.79 |
Reflection shell | Resolution: 2.9→3.07 Å / Num. unique obs: 970 / CC1/2: 0.886 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8H0H Resolution: 2.9→33.86 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3853 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.81 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→33.86 Å
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Refine LS restraints |
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LS refinement shell |
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