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- PDB-7lol: The structure of Agmatinase from E. Coli at 1.8 A displaying urea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lol | ||||||||||||
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Title | The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine | ||||||||||||
![]() | Agmatinase | ||||||||||||
![]() | HYDROLASE | ||||||||||||
Function / homology | ![]() agmatinase / agmatinase activity / putrescine biosynthetic process from arginine / spermidine biosynthetic process / manganese ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Maturana, P. / Figueroa, M. / Gonzalez-Ordenes, F. / Villalobos, P. / Martinez-Oyanedel, J. / Uribe, E.A. / Castro-Fernandez, V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity. Authors: Maturana, P. / Orellana, M.S. / Herrera, S.M. / Martinez, I. / Figueroa, M. / Martinez-Oyanedel, J. / Castro-Fernandez, V. / Uribe, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.7 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7loxC ![]() 3npiS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33593.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 155 molecules ![](data/chem/img/AG2.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AG2 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-URE / | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: Agmatinase at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl2. Condition: 0.1 M phosphate/citrate pH 4.2 and 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.79 Å / Num. obs: 25154 / % possible obs: 99.87 % / Redundancy: 19.9 % / Biso Wilson estimate: 27.14 Å2 / Rmerge(I) obs: 0.06576 / Rrim(I) all: 0.06753 / Net I/σ(I): 28.76 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 2475 / Rrim(I) all: 0.9161 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3NPI Resolution: 1.8→35.79 Å / SU ML: 0.1271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6338 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.79 Å
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Refine LS restraints |
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LS refinement shell |
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