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- PDB-1q74: The Crystal Structure of 1D-myo-inositol 2-acetamido-2-deoxy-alph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q74 | ||||||
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Title | The Crystal Structure of 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB) | ||||||
![]() | 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB) | ||||||
![]() | HYDROLASE / rossmann fold / zinc aminohydrolase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase / N-acetylglucosaminylinositol deacetylase activity / mycothiol biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maynes, J.T. / Garen, C. / Cherney, M.M. / Newton, G. / Arad, D. / Av-Gay, Y. / Fahey, R.C. / James, M.N. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: The Crystal Structure of 1-D-myo-Inositol 2-Acetamido-2-deoxy-alpha-D-glucopyranoside Deacetylase (MshB) from Mycobacterium tuberculosis Reveals a Zinc Hydrolase with a Lactate Dehydrogenase Fold. Authors: Maynes, J.T. / Garen, C. / Cherney, M.M. / Newton, G. / Arad, D. / Av-Gay, Y. / Fahey, R.C. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.9 KB | Display | ![]() |
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PDB format | ![]() | 186.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.4 KB | Display | ![]() |
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Full document | ![]() | 772.5 KB | Display | |
Data in XML | ![]() | 48 KB | Display | |
Data in CIF | ![]() | 70.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31777.230 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PE4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG4000, 50mM Tris-HCl, 0.1M Mg(NO3)2, 6% 1,6-hexanediol and 10% ethyleneglycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2001 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 1331320 / Num. obs: 517484 / % possible obs: 96.3 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 2.2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 |
Reflection shell | Resolution: 1.7→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19275 / Rsym value: 0.296 / % possible all: 95.3 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 134270 / Num. measured all: 1281662 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Lowest resolution: 1.79 Å / % possible obs: 94.7 % |
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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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |