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Yorodumi- PDB-6t8y: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t8y | ||||||
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Title | NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex with the reduced form of the cofactor NADH and the substrate formate at a secondary site. | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | CYTOSOLIC PROTEIN / 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 / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Isupov, M.N. / Yelmazer, B. / De Rose, S.A. / Littlechild, J.A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t8y.cif.gz | 630.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t8y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t8y_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6t8y_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6t8y_validation.xml.gz | 78.3 KB | Display | |
Data in CIF | 6t8y_validation.cif.gz | 118.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8y ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8y | HTTPS FTP |
-Related structure data
Related structure data | 6t8zC 6t92C 6t94C 5dnaS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 45641.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: FDH, CTHT_0067590 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SGU4, formate dehydrogenase |
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-Non-polymers , 5 types, 1914 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG 5000 MME, 2.5 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
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: 1.26→47.06 Å / Num. obs: 407315 / % possible obs: 87 % / Redundancy: 1.7 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 1.5 % / Num. unique obs: 11117 / CC1/2: 0.215 / % possible all: 48.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dna Resolution: 1.26→46.774 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05 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: 23.935 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→46.774 Å
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Refine LS restraints |
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