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- PDB-7esr: Crystal structure of Synechocystis sp PCC6803 guanidinium hydrola... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7esr | ||||||
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Title | Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase (R32) | ||||||
![]() | Probable agmatinase 2 | ||||||
![]() | HYDROLASE / ureohydrolase family protein / arginase/agmatinase family protein / Ni2+ enzyme / 2-metal ion cluster / METAL BINDING PROTEIN | ||||||
Function / homology | ![]() agmatinase / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mayans, O.M. / Fleming, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of a Ni 2+ -dependent guanidine hydrolase in bacteria. Authors: Funck, D. / Sinn, M. / Fleming, J.R. / Stanoppi, M. / Dietrich, J. / Lopez-Igual, R. / Mayans, O. / Hartig, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.7 KB | Display | ![]() |
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PDB format | ![]() | 183.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oi1C ![]() 3nioS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43137.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.06 M (0.3M magnesium chloride hexahydrate, 0.3M calcium chloride dehydrate), 0.1M (1M HEPES; MOPS) pH7.5, 30 % [v/v] (40% [v/v] ethylene glycol, 20% [w/v] PEG 8000) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→28.97 Å / Num. obs: 67577 / % possible obs: 99.03 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.24 |
Reflection shell | Resolution: 1.42→1.43 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1320 / CC1/2: 0.515 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NIO Resolution: 1.42→28.97 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4013 Stereochemistry target values: GeoStd + Monomer Library + 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: 28.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→28.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.38772611308 Å / Origin y: 22.083574978 Å / Origin z: 16.9110270252 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 11 through 601) |