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Yorodumi- PDB-1dli: THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dli | ||||||
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Title | THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION | ||||||
Components | UDP-GLUCOSE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / TERNARY COMPLEX / CRYSTALLOGRAPHIC DIMER | ||||||
Function / homology | Function and homology information UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å | ||||||
Authors | Campbell, R.E. / Mosimann, S.C. / van de Rijn, I. / Tanner, M.E. / Strynadka, N.C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation. Authors: Campbell, R.E. / Mosimann, S.C. / van De Rijn, I. / Tanner, M.E. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dli.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dli.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 1dli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dli_validation.pdf.gz | 557.5 KB | Display | wwPDB validaton report |
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Full document | 1dli_full_validation.pdf.gz | 562.7 KB | Display | |
Data in XML | 1dli_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1dli_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dli ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dli | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45537.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: PGAC147 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0F4, UDP-glucose 6-dehydrogenase |
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-Non-polymers , 5 types, 288 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UDX / | #5: Chemical | #6: 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: 2.54 Å3/Da / Density % sol: 51.66 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: AMMONIUM SULPHATE, GLYCEROL, TRIS-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS Details: ambient temperature | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9057 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→24.23 Å / Num. all: 20008 / Num. obs: 20008 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.377 / % possible all: 76.2 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 24.3 Å / % possible obs: 95.1 % / Num. measured all: 119755 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 76.2 % / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Resolution: 2.31→24.23 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2332306.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.51 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→24.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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