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Yorodumi- PDB-2cdc: Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with N... -
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-Basic information
Entry | Database: PDB / ID: 2cdc | ||||||||||||
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Title | Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and Xylose | ||||||||||||
Components | GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1 | ||||||||||||
Keywords | OXIDOREDUCTASE / GLUCOSE DEHYDROGENASE / REDUCTASE / MDR FAMILY | ||||||||||||
Function / homology | Function and homology information aldose 1-dehydrogenase [NAD(P)+] / xylose binding / galactose catabolic process via D-galactonate / aldose 1-dehydrogenase activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity ...aldose 1-dehydrogenase [NAD(P)+] / xylose binding / galactose catabolic process via D-galactonate / aldose 1-dehydrogenase activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / galactose binding / D-glucose binding / NADP+ binding / NAD+ binding / protein tetramerization / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Milburn, C.C. / Lamble, H.J. / Theodossis, A. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 Title: The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. Authors: Milburn, C.C. / Lamble, H.J. / Theodossis, A. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdc.cif.gz | 339.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdc.ent.gz | 277.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cdc_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2cdc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2cdc_validation.xml.gz | 75.1 KB | Display | |
Data in CIF | 2cdc_validation.cif.gz | 110.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdc ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdc | HTTPS FTP |
-Related structure data
Related structure data | 2cd9SC 2cdaC 2cdbC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40915.254 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET3A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O93715, glucose 1-dehydrogenase [NAD(P)+] |
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-Sugars , 2 types, 10 molecules
#3: Sugar | ChemComp-XYS / #4: Sugar | ChemComp-XYP / |
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-Non-polymers , 4 types, 1595 molecules
#2: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-ZN / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 41 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 41 TO ALA ...ENGINEERED |
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Sequence details | MUTATION OF THR41 TO ALA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Details: 8 % PEG 8000, 0.1 M TRIS (PH 8.0), 4.5 % (V/V) PROPAN-2-OL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.2 Å / Num. obs: 191673 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CD9 Resolution: 1.5→138.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.376 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOP REGIONS ARE DELETED FROM PDB FILE. DISORDERED SIDECHAINS ARE INDICATED BY AND OCCUPANCY OF 0.01
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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: 16.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→138.68 Å
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Refine LS restraints |
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