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Yorodumi- PDB-6f3p: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f3p | ||||||
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Title | Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 6f3p.cif.gz | 436.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f3p.ent.gz | 353 KB | Display | PDB format |
PDBx/mmJSON format | 6f3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f3p_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6f3p_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6f3p_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 6f3p_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3p ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3p | HTTPS FTP |
-Related structure data
Related structure data | 6f3mC 6f3nC 6f3oC 6f3qC 1li4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/M36F3P / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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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: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 10 - 469 / Label seq-ID: 13 - 472
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 51735.031 Da / Num. of mol.: 2 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 , 6 types, 1137 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 50 mM KH2PO4, 15% (W/V) PEG8000, 20% (V/V) GLYCEROL, 2 mM 3'-deoxyadenosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 245319 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.35→1.4 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LI4 Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.337 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / 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: 18.554 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→30 Å
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Refine LS restraints |
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