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- PDB-8ajw: Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ajw | ||||||
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Title | Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations | ||||||
![]() | S-adenosyl-L-homocysteine hydrolase | ||||||
![]() | HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS | ||||||
Function / homology | ![]() adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Drozdzal, P. / Wozniak, K. / Malecki, P. / Gawel, M. / Komorowska, M. / Brzezinski, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations Authors: Drozdzal, P. / Wozniak, K. / Malecki, P. / Gawel, M. / Komorowska, M. / Brzezinski, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 712.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 79.2 KB | Display | |
Data in CIF | ![]() | 115.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f3mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: Beg auth comp-ID: GLY / Beg label comp-ID: GLY
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 51721.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1337 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ADN / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol |
-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: Jun 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.819→79.133 Å / Num. obs: 171257 / % possible obs: 99.7 % / Redundancy: 6.87 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.05 |
Reflection shell | Resolution: 1.819→1.917 Å / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 27398 / CC1/2: 0.683 / Rrim(I) all: 0.156 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F3M Resolution: 1.819→79.133 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.715 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.109 / Details: HYDROGEN ATOMS WERE ADDED AT 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.188 Å2
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Refinement step | Cycle: LAST / Resolution: 1.819→79.133 Å
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Refine LS restraints |
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