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- PDB-5y8m: Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (Mt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y8m | ||||||
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Title | Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + (R)-3-hydroxyisobutyrate (R-HIBA) | ||||||
![]() | Probable 3-hydroxyisobutyrate dehydrogenase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srikalaivani, R. / Singh, A. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Structure, interactions and action ofMycobacterium tuberculosis3-hydroxyisobutyric acid dehydrogenase. Authors: Srikalaivani, R. / Singh, A. / Vijayan, M. / Surolia, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5y8gC ![]() 5y8hC ![]() 5y8iC ![]() 5y8jC ![]() 5y8kC ![]() 5y8lC ![]() 5y8nC ![]() 5y8oC ![]() 5y8pC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29837.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25618 / H37Rv / Gene: mmsB, Rv0751c, MTV041.25c / Plasmid: pET22b / Production host: ![]() ![]() ![]() References: UniProt: P9WNY5, ![]() |
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-Non-polymers , 6 types, 559 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/9ON.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HIU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/9ON.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HIU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-AKR / | ![]() #4: Chemical | #5: Chemical | ChemComp-NAD / | ![]() #6: Chemical | ChemComp-HIU / ( | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow![]() | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: 0.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.04→111.73 Å / Num. obs: 42572 / % possible obs: 99.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.04→2.15 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 11.2 / Num. unique obs: 42572 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 21.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→111.73 Å
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Refine LS restraints |
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