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Yorodumi- PDB-4gmh: Crystal structure of staphylococcus aureus 5'-methylthioadenosine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gmh | ||||||
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Title | Crystal structure of staphylococcus aureus 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase | ||||||
Components | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
Keywords | HYDROLASE / NUCLEOSIDASE / MTAN / ALPHA/BETA PROTEINS / S-ADENOSYLHOMOCYSTEINE / CLEAVAGE | ||||||
Function / homology | Function and homology information adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Brown, R.L. / Anderson, B.F. / Norris, G.E. / Tyler, P.C. / Evans, G.B. / Sutherland-Smith, A.J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of staphylococcus aureus 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase Authors: Brown, R.L. / Anderson, B.F. / Norris, G.E. / Tyler, P.C. / Evans, G.B. / Sutherland-Smith, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gmh.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmh.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmh ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmh | HTTPS FTP |
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-Related structure data
Related structure data | 3bl6S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24698.191 Da / Num. of mol.: 1 / Fragment: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: MU50 / Gene: mtnN, SAV1599 / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99TQ0, adenosylhomocysteine nucleosidase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.93 % |
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Crystal grow | pH: 8.5 Details: 4.2M FORMATE, 0.1M TRIS HCL, CRYOPROTECTANT 20% GLYCEROL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 110K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.5418 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 17, 2007 |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→27.93 Å / Num. obs: 18068 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.91 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 3.49 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.23 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: S AUREUS MTAN 3BL6 Resolution: 2→26.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.132 / SU ML: 0.115 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: ENGH & HUBER Details: HYDROGENS HAVE BEEN ADDED IN THEIR 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.331 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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