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Yorodumi- PDB-6ayq: Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ayq | ||||||
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Title | Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A | ||||||
Components | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
Keywords | HYDROLASE / TRANSFERASE / MTAN enzyme / Foodborne Diseases | ||||||
Function / homology | Function and homology information aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Cameron, S.A. / Harijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Transition-State Analogues of Campylobacter jejuni 5'-Methylthioadenosine Nucleosidase. Authors: Ducati, R.G. / Harijan, R.K. / Cameron, S.A. / Tyler, P.C. / Evans, G.B. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ayq.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayq.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ayq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ayq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ayq_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6ayq_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayq ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayq | HTTPS FTP |
-Related structure data
Related structure data | 6aymC 6ayoC 6ayrC 6aysC 6aytC 4wknS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26312.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0M70_07260, AJY53_05400 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1E7P7U4, UniProt: Q0PC20*PLUS, adenosylhomocysteine nucleosidase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.1 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Bis-Tris pH 6.5, 28% (w/v) PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2016 |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→65.65 Å / Num. obs: 81192 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.99 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.42→1.45 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4310 / CC1/2: 0.71 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WKN Resolution: 1.42→65.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.286 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / 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: 18.686 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→65.65 Å
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Refine LS restraints |
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