+Open data
-Basic information
Entry | Database: PDB / ID: 2d2x | ||||||
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Title | Crystal structure of 2-deoxy-scyllo-inosose synthase | ||||||
Components | 2-deoxy-scyllo-inosose synthase | ||||||
Keywords | LYASE / aminoglycoside / 2-deoxystreptamine / dehydroquinate synthase | ||||||
Function / homology | Function and homology information 2-deoxy-scyllo-inosose synthase / 3-dehydroquinate synthase activity / aromatic amino acid family biosynthetic process / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Nango, E. / Kumasaka, T. / Tanaka, N. / Kakinuma, K. / Eguchi, T. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+ Authors: Nango, E. / Kumasaka, T. / Hirayama, T. / Tanaka, N. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d2x.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d2x.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 2d2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2x ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2x | HTTPS FTP |
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-Related 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: 40792.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Plasmid: PET30B / Production host: Escherichia coli (E. coli) References: UniProt: Q9S5E2, Lyases; Carbon-oxygen lyases; Acting on phosphates #2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 40%(w/v) PEG 4000, 200mM Li2SO4, 100mM Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→24.77 Å / Num. all: 36626 / Num. obs: 36626 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→24.77 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→24.77 Å
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