[English] 日本語
Yorodumi- PDB-6t8z: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t8z | ||||||
---|---|---|---|---|---|---|---|
Title | NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A ternary complex with the oxidised form of the cofactor NAD+ and the substrate formate both at a primary and secondary sites. | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | CYTOSOLIC PROTEIN / NAD+ dependent 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6t8z.cif.gz | 631.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6t8z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t8z_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6t8z_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 6t8z_validation.xml.gz | 78.8 KB | Display | |
Data in CIF | 6t8z_validation.cif.gz | 119.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8z ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8z | HTTPS FTP |
-Related structure data
Related structure data | 6t8yC 6t92C 6t94C 5dnaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
|
-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 |
---|
-Non-polymers , 5 types, 1991 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 0.1M Bis-Tris, pH 5.5, 25 % w/v PEG 3350, 2.5 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 1.21→47.03 Å / Num. obs: 467507 / % possible obs: 89.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 1.8 % / Num. unique obs: 22684 / CC1/2: 0.25 / Χ2: 0.7 / % possible all: 87.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dna Resolution: 1.21→47.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.049 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.293 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→47.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|