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Yorodumi- PDB-5h8i: Crystal structure of Medicago truncatula N-carbamoylputrescine am... -
+Open data
-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 | ||||||
Components | N-carbamoylputrescine amidohydrolase | ||||||
Keywords | HYDROLASE / amidase / helical octamer / alpha-beta-beta-alpha sandwich fold / intermediate | ||||||
Function / homology | Function and homology information N-carbamoylputrescine amidase / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Front Plant Sci / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h8i.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5h8i.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5h8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/5h8i ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h8i | HTTPS FTP |
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-Related structure data
Related structure data | 5h8jC 5h8kC 5h8lC 1erzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Medicago truncatula (barrel medic) / Gene: MTR_2g086600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: G7ITU5, N-carbamoylputrescine amidase |
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-Non-polymers , 7 types, 4463 molecules
#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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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