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Yorodumi- PDB-5b7g: Structures and functional analysis of periplasmic 5-methylthioade... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b7g | ||||||||||||||||||
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Title | Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila | ||||||||||||||||||
Components | MTA/SAH nucleosidase | ||||||||||||||||||
Keywords | HYDROLASE / Aeromonas hydrophila / MtaN-1 / MtaN-2 / SAH / MTA / 5-DAO | ||||||||||||||||||
Function / homology | Function and homology information methylthioadenosine nucleosidase / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside metabolic process / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å | ||||||||||||||||||
Authors | Xu, Y. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila. Authors: Xu, Y. / Wang, L. / Chen, J. / Zhao, J. / Fan, S. / Dong, Y. / Ha, N.C. / Quan, C. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b7g.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b7g.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 5b7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b7g_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
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Full document | 5b7g_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 5b7g_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 5b7g_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b7g ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b7g | HTTPS FTP |
-Related structure data
Related structure data | 5b7nC 5b7pC 5b7qC 3nm4S 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: 27235.615 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: ATCC 7966 / DSM 30187 / Gene: mtnN-1, AHA_0953 / Production host: Escherichia coli (E. coli) References: UniProt: A0KGU9, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase #2: Chemical | #3: Chemical | #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: 3.32 Å3/Da / Density % sol: 62.95 % |
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Crystal grow | Temperature: 288 K / Method: evaporation / pH: 4.6 Details: 6% (w/v) polyethylene glycol 4000, 0.1 M sodium acetate trihydrate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→49.49 Å / Num. obs: 142443 / % possible obs: 99.2 % / Redundancy: 6.5 % / Net I/σ(I): 14.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NM4 Resolution: 1.399→29.639 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.399→29.639 Å
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Refine LS restraints |
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LS refinement shell |
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