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Yorodumi- PDB-8cfz: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cfz | ||||||
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Title | Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H09 | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / Fragment screening / protein-ligand complex / drug discovery / SAM-DEPENDENT METHYLATION REACTIONS / SAHase / AHCY | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Malecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To be published Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry H09 Authors: Malecki, P.H. / Gawel, M. / Stepniewska, 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 | 8cfz.cif.gz | 873.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cfz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cfz_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 8cfz_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 8cfz_validation.xml.gz | 164.6 KB | Display | |
Data in CIF | 8cfz_validation.cif.gz | 243.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfz ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfz | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDHIJK
#1: Protein | Mass: 51735.031 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase |
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-Non-polymers , 7 types, 3360 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ADE / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-A1H8H / Mass: 225.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9F2N3O / Feature type: SUBJECT OF INVESTIGATION #7: Chemical | ChemComp-GOL / #8: 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: 3.03 Å3/Da / Density % sol: 59.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 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: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 27, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→48.53 Å / Num. obs: 470138 / % possible obs: 98.2 % / Redundancy: 4.67 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.13 / Net I/σ(I): 9.69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→43.42 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4005 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→43.42 Å
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Refine LS restraints |
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LS refinement shell |
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