+Open data
-Basic information
Entry | Database: PDB / ID: 1gco | ||||||
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Title | CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE COMPLEXED WITH NAD+ | ||||||
Components | GLUCOSE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / sporulation resulting in formation of a cellular spore Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. | ||||||
Citation | Journal: J.Biochem. / Year: 2001 Title: Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution. Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3 Authors: Yamamoto, K. / Kusunoki, M. / Urabe, I. / Tabata, S. / Osaki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gco.cif.gz | 216.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gco.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gco_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1gco_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1gco_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 1gco_validation.cif.gz | 62.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gco ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gco | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28112.963 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) References: UniProt: P40288, glucose 1-dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-NAD / #3: 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: 2.13 Å3/Da / Density % sol: 42.26 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG2000, sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 KDetails: used microseeding, Yamamoto, K., (2000) Acta Crystallogr., Sect.D, 56, 1443. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 357354 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 3.77 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.166 / Num. unique all: 8013 / % possible all: 77.3 |
Reflection | *PLUS Num. obs: 94821 / Num. measured all: 357354 |
Reflection shell | *PLUS % possible obs: 77.3 % / Mean I/σ(I) obs: 11.2 |
-Processing
Software |
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Refinement | Resolution: 1.7→34.39 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2894287.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5391 Å2 / ksol: 0.314666 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→34.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.241 / % reflection Rfree: 5 % / Rfactor Rwork: 0.216 |