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- PDB-6t92: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t92 | ||||||
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Title | NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH and the substrate formate at a secondary site. | ||||||
![]() | Formate dehydrogenase | ||||||
![]() | CYTOSOLIC PROTEIN / NAD+ | ||||||
Function / homology | ![]() 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 / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isupov, M.N. / Yelmazer, B. / De Rose, S.A. / Littlechild, J.A. | ||||||
![]() | ![]() Title: Structural insights into the NAD + -dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD + ternary complex of the Chaetomium thermophilum enzyme. Authors: Yilmazer, B. / Isupov, M.N. / De Rose, S.A. / Bulut, H. / Benninghoff, J.C. / Binay, B. / Littlechild, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 616.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 75 KB | Display | |
Data in CIF | ![]() | 113.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t8yC ![]() 6t8zC ![]() 6t94C ![]() 5dnaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 45630.441 Da / Num. of mol.: 4 / Mutation: N120C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: FDH, CTHT_0067590 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 1781 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 10 % w/v PEG 1000, 10 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→63.93 Å / Num. obs: 548213 / % possible obs: 82.1 % / Redundancy: 1.7 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.998 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 17604 / CC1/2: 0.291 / % possible all: 53.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5dna Resolution: 1.12→63.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.109 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→63.93 Å
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Refine LS restraints |
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