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- PDB-7lox: The structure of Agmatinase from E. Coli at 3.2 A displaying guan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lox | ||||||||||||
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Title | The structure of Agmatinase from E. Coli at 3.2 A displaying guanidine in the active site | ||||||||||||
![]() | 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 | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lolC ![]() 3npiS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 33593.988 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GAI / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl. Crystallization: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350 |
-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: 1.771 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→64.51 Å / Num. obs: 14314 / % possible obs: 99.87 % / Redundancy: 39.4 % / Biso Wilson estimate: 84.61 Å2 / Rmerge(I) obs: 0.1561 / Rrim(I) all: 0.1582 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 3.2→3.314 Å / Rmerge(I) obs: 0.1561 / Num. unique obs: 1418 / Rrim(I) all: 0.1582 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NPI Resolution: 3.2→64.51 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8165 / 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: 81.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→64.51 Å
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Refine LS restraints |
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LS refinement shell |
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