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Yorodumi- PDB-2gug: NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gug | ||||||
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Title | NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (ALDEHUDE (D) / NAD+(A)) | ||||||
Function / homology | Function and homology information formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 2.28 Å | ||||||
Authors | Filippova, E.V. / Polyakov, K.M. / Tikhonova, T.V. / Boiko, K.M. / Tishkov, V.I. / Popov, V.O. | ||||||
Citation | Journal: KRISTALLOGRAFIYA / Year: 2006 Title: Crystal structure of the complex of NAD-dependent formate dehydrogenase from metylotrophic bacterium Pseudomonas sp.101 with formate. Authors: Filippova, E.V. / Polyakov, K.M. / Tikhonova, T.V. / Stekhanova, T.N. / Boiko, K.M. / Sadihov, I.G. / Tishkov, V.I. / Labrou, N. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gug.cif.gz | 299.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gug.ent.gz | 243.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gug_validation.pdf.gz | 499.4 KB | Display | wwPDB validaton report |
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Full document | 2gug_full_validation.pdf.gz | 530.3 KB | Display | |
Data in XML | 2gug_validation.xml.gz | 58.8 KB | Display | |
Data in CIF | 2gug_validation.cif.gz | 81.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/2gug ftp://data.pdbj.org/pub/pdb/validation_reports/gu/2gug | HTTPS FTP |
-Related structure data
Related structure data | 2nacS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44242.090 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: 101 / Plasmid: pPsFDH8a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P33160, formate dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: 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: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.8% PEG400, 2M Na formate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8019 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8019 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→16.1 Å / Num. obs: 73290 / % possible obs: 97.9 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MOLREP Starting model: pdb entry 2NAC Resolution: 2.28→100 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.933 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.737 Å2
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Refine analyze | Luzzati sigma a obs: 0.292 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.34 Å / Total num. of bins used: 20
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