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Yorodumi- PDB-8am6: Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrifica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8am6 | ||||||
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Title | Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate cyclohex-2-en-1-one - inactive mutant (Y195F) | ||||||
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: 1.33 Å | ||||||
Authors | Prior, S.H. / Taylor, E.J. | ||||||
Funding support | United Kingdom, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8am6.cif.gz | 282.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8am6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8am6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8am6_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 8am6_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8am6_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 8am6_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8am6 ftp://data.pdbj.org/pub/pdb/validation_reports/am/8am6 | HTTPS FTP |
-Related structure data
Related structure data | 8am3SC 8am8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
-Components
-Protein , 1 types, 2 molecules AAABaB
#1: Protein | Mass: 64553.590 Da / Num. of mol.: 2 / Mutation: Y195F 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 |
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-Non-polymers , 5 types, 1338 molecules
#2: Chemical | #3: Chemical | ChemComp-A2Q / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #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: 2.67 Å3/Da / Density % sol: 53.96 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→60.932 Å / Num. obs: 290848 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 1 / Rrim(I) all: 0.15 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.33→1.35 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14363 / CC1/2: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8am3 Resolution: 1.33→60.932 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.965 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 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 / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→60.932 Å
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Refine LS restraints |
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LS refinement shell |
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