[English] 日本語
Yorodumi- PDB-8am8: Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrifica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8am8 | ||||||
---|---|---|---|---|---|---|---|
Title | Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate - W113A mutant | ||||||
Components | Fumarate reductase/succinate dehydrogenase flavoprotein domain protein | ||||||
Keywords | FLAVOPROTEIN / FAD / cyclic ketone / enzyme engineering / rational design | ||||||
Function / homology | Function and homology information steroid metabolic process / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Alicycliphilus denitrificans K601 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Prior, S.H. / Taylor, E.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Chem Sci / Year: 2024 Title: Rational design of a cyclohexanone dehydrogenase for enhanced alpha , beta-desaturation and substrate specificity. Authors: Singh, W. / Brown, N.L. / McCue, H.V. / Marriott, S.R. / Wilson, R.C. / Perry, J. / Turkenburg, J.P. / Dubey, K.D. / Prior, S.H. / Carnell, A.J. / Taylor, E.J. / Black, G.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8am8.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8am8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8am8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8am8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8am8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8am8_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 8am8_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8am8 ftp://data.pdbj.org/pub/pdb/validation_reports/am/8am8 | HTTPS FTP |
-Related structure data
Related structure data | 8am3SC 8am6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains BBB AAA) |
-Components
-Protein , 1 types, 2 molecules BBBAAA
#1: Protein | Mass: 64454.457 Da / Num. of mol.: 2 / Mutation: W113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicycliphilus denitrificans K601 (bacteria) Gene: Alide2_4318 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4G7N3 |
---|
-Non-polymers , 6 types, 674 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 240 mM ammonium citrate tribasic 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→85.65 Å / Num. obs: 98195 / % possible obs: 99.88 % / Redundancy: 2.6 % / Biso Wilson estimate: 20.861 Å2 / CC1/2: 0.973 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4779 / CC1/2: 0.999 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8am3 Resolution: 1.85→85.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.651 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 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 / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.769 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→85.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|