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Yorodumi- PDB-6f3q: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f3q | ||||||
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Title | Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenine and Rb+ cation | ||||||
Components | Adenosylhomocysteinase | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Czyrko, J. / Brzezinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f3q.cif.gz | 820.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f3q.ent.gz | 677.3 KB | Display | PDB format |
PDBx/mmJSON format | 6f3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3q ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3q | HTTPS FTP |
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-Related structure data
Related structure data | 6f3mC 6f3nC 6f3oC 6f3pSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/M36F3Q / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 51735.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase |
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-Non-polymers , 7 types, 2151 molecules
#2: Chemical | ChemComp-RB / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-ADE / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 50 mM RbH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8077 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016 / Details: Si-111 crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8077 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 318355 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.45→1.54 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F3P Resolution: 1.45→48.53 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.698 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.042 / 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: 16.59 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→48.53 Å
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Refine LS restraints |
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