[English] 日本語
Yorodumi- PDB-6fk3: Structure and function of aldehyde dehydrogenase from Thermus the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fk3 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Recombinant full-length protein in complex with propanal) | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / aldehyde dehydrogenase / Thermus thermophilus | ||||||
Function / homology | Function and homology information phenylacetaldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hayes, K.A. / Noor, M.R. / Djeghader, A. / Soulimane, T. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Authors: Hayes, K. / Noor, M. / Djeghader, A. / Armshaw, P. / Pembroke, T. / Tofail, S. / Soulimane, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fk3.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fk3.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fk3_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fk3_full_validation.pdf.gz | 500.7 KB | Display | |
Data in XML | 6fk3_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 6fk3_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fk3 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fk3 | HTTPS FTP |
-Related structure data
Related structure data | 6fjxC 6fkuC 6fkvC 4wj9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 530 / Label seq-ID: 7 - 536
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59451.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0513 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72KD3, aldehyde dehydrogenase (NAD+) |
---|
-Non-polymers , 6 types, 248 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MPO / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.38 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 50 mM MOPS pH 7.5 and 1.2 M ammonium sulfate, 50 mM propanal |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→74.405 Å / Num. all: 2851615 / Num. obs: 79663 / % possible obs: 99.4 % / Redundancy: 25.5 % / Rmerge(I) obs: 0.2859 / Net I/σ(I): 9.24 |
Reflection shell | Resolution: 2.05→2.123 Å / Rmerge(I) obs: 6.405 / Num. unique all: 7805 / % possible all: 97.39 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WJ9 Resolution: 2.3→48.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.233 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.667 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→48.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|