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Yorodumi- PDB-6tb6: Crystal structure of formate dehydrogenase FDH2 D222S/Q223R enzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tb6 | ||||||
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Title | Crystal structure of formate dehydrogenase FDH2 D222S/Q223R enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP and azide. | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / formate dehydrogenase / NAD / 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: 1.98 Å | ||||||
Authors | Robescu, M.S. / Rubini, R. / Filippini, F. / Bergantino, B. / Cendron, L. | ||||||
Citation | Journal: Chemcatchem / Year: 2020 Title: From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice Authors: Robescu, M.S. / Rubini, R. / Beneventi, E. / Tavanti, M. / Lonigro, C. / Zito, F. / Filippini, F. / 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 | 6tb6.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tb6.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tb6_validation.pdf.gz | 957.5 KB | Display | wwPDB validaton report |
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Full document | 6tb6_full_validation.pdf.gz | 960.8 KB | Display | |
Data in XML | 6tb6_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 6tb6_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tb6 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tb6 | HTTPS FTP |
-Related structure data
Related structure data | 6t8cSC 6t9wC 6t9xC 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 42590.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Granulicella mallensis (bacteria) / Gene: AciX8_0868 / Production host: Escherichia coli (E. coli) / References: UniProt: G8NTI5, formate dehydrogenase |
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-Non-polymers , 5 types, 386 molecules
#2: Chemical | ChemComp-AZI / | ||||
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#3: Chemical | ChemComp-NAP / | ||||
#4: Chemical | #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Cadmium chloride hemi(pentahydrate), 0.005 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES pH 7.5, 12 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→45.67 Å / Num. all: 28252 / Num. obs: 207048 / % possible obs: 99.87 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 7.46 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 6.3 / Num. unique all: 30645 / Num. unique obs: 2791 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6T8C Resolution: 1.98→35.585 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 63.1 Å2 / Biso mean: 24.9831 Å2 / Biso min: 12.54 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→35.585 Å
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LS refinement shell | Resolution: 1.98→2.0181 Å / Rfactor Rfree error: 0
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