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Yorodumi- PDB-2vwq: Haloferax mediterranei glucose dehydrogenase in complex with NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vwq | ||||||
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Title | Haloferax mediterranei glucose dehydrogenase in complex with NADP and Zn. | ||||||
Components | GLUCOSE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GLUCOSE DEHYDROGENASE / ZINC DEPENDENT MEDIUM CHAIN ALCOHOL DEHYDROGENASE FAMILY / ALCOHOL DEHYDROGENASE | ||||||
Function / homology | Function and homology information 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 | HALOFERAX MEDITERRANEI (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Baker, P.J. / Britton, K.L. / Fisher, M. / Esclapez, J. / Pire, C. / Bonete, M.J. / Ferrer, J. / Rice, D.W. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2009 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vwq.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwq.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vwq_validation.pdf.gz | 741.1 KB | Display | wwPDB validaton report |
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Full document | 2vwq_full_validation.pdf.gz | 741.3 KB | Display | |
Data in XML | 2vwq_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 2vwq_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwq ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwq | HTTPS FTP |
-Related structure data
Related structure data | 2vwgC 2vwhC 2vwpC 2b5vS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 39282.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOFERAX MEDITERRANEI (archaea) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q977U7, glucose 1-dehydrogenase [NAD(P)+] |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 1.6M SODIUM CITRATE, 0.1M NAHEPES PH8.0, 10MM NADP |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 2001 / Details: 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: 2.1→30 Å / Num. obs: 33219 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B5V Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.162 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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