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Yorodumi- PDB-1h6c: Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Z... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h6c | ||||||
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Title | Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas mobilis complexed with succinate | ||||||
Components | PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE | ||||||
Keywords | PROTEIN TRANSLOCATION / PERIPLASMIC OXIDOREDUCTASE / SIGNAL PEPTIDE / LIGAND BINDING | ||||||
Function / homology | Function and homology information glucose-fructose oxidoreductase / sorbitol biosynthetic process / glucose-fructose oxidoreductase activity / periplasmic space / nucleotide binding Similarity search - Function | ||||||
Biological species | ZYMOMONAS MOBILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nurizzo, D. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal Structures of the Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas Mobilis and its Complexes with Bound Ligands Authors: Nurizzo, D. / Halbig, D. / Sprenger, G. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h6c.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6c.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6c ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6c | HTTPS FTP |
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-Related structure data
Related structure data | 1h6aC 1h6bC 1h6dC 1ofgS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 47342.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NADP, SUCCINATE, GLYCEROL / Source: (gene. exp.) ZYMOMONAS MOBILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P75002, UniProt: Q07982*PLUS, glucose-fructose oxidoreductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | MATURE FORM OF GLUCOSE FRUCTOSE OXIDOREDUC | |
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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: 2.62 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 12% PEG6000, 210MM AMMONIUM SULFATE, 20% GLYCEROL, 100MM K-SUCCINATE PH6.5, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: DOUBLE FOCUSING MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 46439 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OFG Resolution: 2.2→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1999823 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.4782 Å2 / ksol: 0.327656 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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