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Yorodumi- PDB-6mt1: Crystal structure of Inorganic Pyrophosphatase from Medicago trun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mt1 | ||||||
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Title | Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (R3 crystal form) | ||||||
Components | Soluble inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / pyrophosphate / PPA / autoproteolysis | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Ruszkowski, M. / Grzechowiak, M. / Dauter, Z. | ||||||
Citation | Journal: Biochem.J. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mt1.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mt1.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mt1 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mt1 | HTTPS FTP |
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-Related structure data
Related structure data | 5ls0C 6mt2C 4lugS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25500596, MTR_8g024050 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A072TMB0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.6% Tacsimate pH 5.0, 80 mM Na Citrate tribasic pH 5.6, 12.8% PEG 3350, 20% Glycerol Bromelain 5 ug/ml MtPPA1 7.7 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2017 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 37764 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Net I/σ(I): 17.22 |
Reflection shell | Resolution: 1.84→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5879 / CC1/2: 0.79 / Rrim(I) all: 0.96 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lug Resolution: 1.84→40.89 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 7.394 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / 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: 50.482 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→40.89 Å
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Refine LS restraints |
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