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- PDB-3h7c: Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h7c | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression | ||||||
![]() | Agmatine deiminase | ||||||
![]() | HYDROLASE / Agmatine / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / N-carbamoylputrescine / Arginine decarboxylase pathway / Polyamine biosynthesis | ||||||
Function / homology | ![]() agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process from arginine / polyamine biosynthetic process / protein-arginine deiminase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
![]() | ![]() Title: Structural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase Authors: Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.7 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 30 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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Details | biological unit is the same as asymmetric unit. |
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Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 43430.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cell free synthesis / Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 7 types, 370 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/211.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/211.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-211 / | #7: Chemical | ChemComp-1PE / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE SEQUENCE MATCHES GENBANK ENTRY AAO63405.1. THE DISCREPANCY BETWEEN AUTHOR'S ...AUTHORS STATE THAT THE SEQUENCE MATCHES GENBANK ENTRY AAO63405.1. THE DISCREPANC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; ...Details: Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; Cryoprotectant- MiTeGen LV Cryo Oil, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 68398 / Num. obs: 68398 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.6 | ||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3395 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.57 Å2 / Biso mean: 14.686 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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