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- PDB-6mt2: Crystal structure of Inorganic Pyrophosphatase from Medicago trun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mt2 | ||||||
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Title | Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (I23 crystal form) | ||||||
![]() | Soluble inorganic pyrophosphatase | ||||||
![]() | HYDROLASE / pyrophosphate / PPA / autoproteolysis | ||||||
Function / homology | ![]() inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruszkowski, M. / Grzechowiak, M. / Dauter, Z. | ||||||
![]() | ![]() Title: Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity. Authors: Grzechowiak, M. / Ruszkowski, M. / Sliwiak, J. / Szpotkowski, K. / Sikorski, M. / Jaskolski, 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 | ![]() | 295 KB | Display | ![]() |
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PDB format | ![]() | 244.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ls0C ![]() 6mt1C ![]() 4lugS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24656.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: A0A072TMB0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.5 Å3/Da / Density % sol: 81.45 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 4% Tacsimate pH 6.0, 12% PEG 3350 crystal after 3 months 20% Ethylene glycol as cryoprotectant MtPPA1 at 16.3 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 11, 2016 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→50 Å / Num. obs: 48141 / % possible obs: 99.7 % / Redundancy: 16 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.14 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.89→3.07 Å / Redundancy: 15 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7620 / CC1/2: 0.65 / Rrim(I) all: 1.8 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4lug Resolution: 2.89→48.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.492 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.2 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.382 Å2
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Refinement step | Cycle: 1 / Resolution: 2.89→48.01 Å
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Refine LS restraints |
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