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Yorodumi- PDB-4xye: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xye | ||||||
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Title | GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+) | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / FORMATE DEHYDROGENASE / NAD | ||||||
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 | Granulicella mallensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cendron, L. / Fogal, S. / Beneventi, E. / Bergantino, E. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2015 Title: Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8. Authors: Fogal, S. / Beneventi, E. / Cendron, L. / Bergantino, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xye.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xye.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xye_validation.pdf.gz | 980.4 KB | Display | wwPDB validaton report |
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Full document | 4xye_full_validation.pdf.gz | 986.6 KB | Display | |
Data in XML | 4xye_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 4xye_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xye ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xye | HTTPS FTP |
-Related structure data
Related structure data | 4xybC 4xygC 2nacS 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: 42809.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8) (bacteria) Gene: AciX8_2172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8NVB5, formate dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Mes pH 6.5, 12 % w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.98 Å / Num. obs: 78950 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NAC Resolution: 1.8→40.98 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.98 Å
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Refine LS restraints |
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LS refinement shell |
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