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- PDB-6f3m: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f3m | ||||||
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Title | Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenosine, K+ and Zn2+ cations | ||||||
![]() | (Adenosylhomocysteinase) x 2 | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Czyrko, J. / Brzezinski, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Authors: Czyrko, J. / Sliwiak, J. / Imiolczyk, B. / Gdaniec, Z. / Jaskolski, 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 | ![]() | 757 KB | Display | ![]() |
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PDB format | ![]() | 619.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 84.8 KB | Display | |
Data in CIF | ![]() | 129.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f3nC ![]() 6f3oC ![]() 6f3pSC ![]() 6f3qC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: _
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 50673.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: ![]() ![]() |
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#2: Protein | Mass: 50616.758 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: ![]() ![]() |
-Non-polymers , 7 types, 1998 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-ADN / #5: Chemical | #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-K / #8: Chemical | ChemComp-ZN / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 50 mM KH2PO4, 20 % (W/V) PEG8000, 2 mM adenosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 244909 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.6→1.69 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F3P Resolution: 1.6→48.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.011 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.431 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→48.7 Å
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Refine LS restraints |
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