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Yorodumi- PDB-8ajw: Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine... -
+Open data
-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 | ||||||
Components | S-adenosyl-L-homocysteine hydrolase | ||||||
Keywords | HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 Å | ||||||
Authors | Drozdzal, P. / Wozniak, K. / Malecki, P. / Gawel, M. / Komorowska, M. / Brzezinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ajw.cif.gz | 712.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ajw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ajw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/8ajw ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8ajw | HTTPS FTP |
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-Related structure data
Related structure data | 6f3mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / Variant (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685 |
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-Non-polymers , 5 types, 1337 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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