+Open data
-Basic information
Entry | Database: PDB / ID: 4xyg | ||||||
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Title | GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / FORMATE DEHYDROGENASE | ||||||
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: 1.7 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 | 4xyg.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyg.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xyg_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 4xyg_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 4xyg_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4xyg_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyg ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyg | HTTPS FTP |
-Related structure data
Related structure data | 4xybC 4xyeC 2nacS 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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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
-Components
#1: Protein | Mass: 42809.738 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) / References: UniProt: G8NVB5, formate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.01 M Nickel Chloride, 0.1 M TRIS pH 8.5, 20 %(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: 1.7→34.02 Å / Num. obs: 42594 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NAC Resolution: 1.7→34.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.46 / 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: 1.7→34.02 Å
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Refine LS restraints |
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LS refinement shell |
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