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- PDB-5h8i: Crystal structure of Medicago truncatula N-carbamoylputrescine am... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h8i | ||||||
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Title | Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine | ||||||
![]() | N-carbamoylputrescine amidohydrolase | ||||||
![]() | HYDROLASE / amidase / helical octamer / alpha-beta-beta-alpha sandwich fold / intermediate | ||||||
Function / homology | ![]() N-carbamoylputrescine amidase / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. Authors: Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 621.5 KB | Display | ![]() |
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Full document | ![]() | 665.1 KB | Display | |
Data in XML | ![]() | 210.1 KB | Display | |
Data in CIF | ![]() | 304.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h8jC ![]() 5h8kC ![]() 5h8lC ![]() 1erzS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 34130.660 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 4463 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/N2H.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/N2H.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-PGE / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-N2H / ( #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG3350, 8% Tacsimate at pH 7.0, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 6, 2015 |
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: 1.97→40 Å / Num. obs: 462097 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.45 |
Reflection shell | Resolution: 1.97→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.95 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ERZ Resolution: 1.97→39.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.695 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.576 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→39.55 Å
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Refine LS restraints |
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