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Yorodumi- PDB-4xyb: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NADP(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xyb | ||||||
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Title | GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NADP(+) AND NaN3 | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / FORMATE DEHYDROGENASE / NADP | ||||||
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: 1.38 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 | 4xyb.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyb.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xyb_validation.pdf.gz | 963.4 KB | Display | wwPDB validaton report |
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Full document | 4xyb_full_validation.pdf.gz | 968.5 KB | Display | |
Data in XML | 4xyb_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 4xyb_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyb ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyb | HTTPS FTP |
-Related 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) Strain: ATCC BAA-1857 / DSM 23137 / MP5ACTX8 / Gene: AciX8_2172 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8NVB5, formate dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Na Acetate 2.0 M Formate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012 / Details: Focusing optics: Toroidal mirror |
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: 1.38→40.64 Å / Num. obs: 154449 / % possible obs: 97.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.25 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.38→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.4 / % possible all: 82.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→31 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.31 / 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: 1.38→31 Å
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Refine LS restraints |
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LS refinement shell |
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