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- PDB-1mp2: Structure of MT-ADPRase (Apoenzyme), a Nudix hydrolase from Mycob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mp2 | ||||||
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Title | Structure of MT-ADPRase (Apoenzyme), a Nudix hydrolase from Mycobacterium tuberculosis | ||||||
![]() | ADPR pyrophosphatase | ||||||
![]() | HYDROLASE / Rv1700 / ADPRase / Nudix hydrolase / ADPR / Mycobacterium Tuberculosis | ||||||
Function / homology | ![]() guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / UDP-sugar diphosphatase activity / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kang, L.-W. / Gabelli, S.B. / Bianchet, M.A. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M. | ||||||
![]() | ![]() Title: Structure and mechanism of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis Authors: Kang, L.-W. / Gabelli, S.B. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.3 KB | Display | ![]() |
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PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 361.3 KB | Display | ![]() |
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Full document | ![]() | 365.2 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22920.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.88 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na Formate, Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 23, 2001 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 18295 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.099 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 8.43 / Rsym value: 0.317 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 146287 / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 8.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.262 / Rfactor Rwork: 0.204 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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