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- PDB-2vwp: Haloferax mediterranei glucose dehydrogenase in complex with NADP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vwp | ||||||
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Title | Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn. | ||||||
![]() | GLUCOSE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / GLUCOSE DEHYDROGENASE / ZINC DEPENDENT MEDIUM CHAIN ALCOHOL DEHYDROGENASE FAMILY / ALCOHOL DEHYDROGENASE | ||||||
Function / homology | ![]() 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 / D-glucose binding / NADP+ binding / NAD+ binding / protein homodimerization activity / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Baker, P.J. / Britton, K.L. / Fisher, M. / Esclapez, J. / Pire, C. / Bonete, M.J. / Ferrer, J. / Rice, D.W. | ||||||
![]() | ![]() Title: Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily. Authors: Baker, P.J. / Britton, K.L. / Fisher, M. / Esclapez, J. / Pire, C. / Bonete, M.J. / Ferrer, J. / Rice, D.W. | ||||||
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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.8 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 714.2 KB | Display | ![]() |
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Full document | ![]() | 714.6 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vwgC ![]() 2vwhC ![]() 2vwqC ![]() 2b5vS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39282.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q977U7, glucose 1-dehydrogenase [NAD(P)+] |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 70% 2-METHYL-2,4,-PENTANEDIOL, 1MM NADPH, 1MM ZNCL2, 100MM HEPES PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2001 / Details: YALE MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→30 Å / Num. obs: 32173 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.7 / % possible all: 82.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B5V Resolution: 2.01→19.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.581 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→19.84 Å
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Refine LS restraints |
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