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- PDB-8d4w: Asymmetric ene-reduction of alpha,beta-unsaturated compounds usin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d4w | ||||||
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Title | Asymmetric ene-reduction of alpha,beta-unsaturated compounds using MSMEG_2850 | ||||||
![]() | Cell entry (Mce) related family protein | ||||||
![]() | OXIDOREDUCTASE / F420 / FDOR | ||||||
Function / homology | F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / FMN-binding split barrel / Oxidoreductases / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / Cell entry (Mce) related family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, S.W. / Frkic, R.L. / Jackson, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Asymmetric Ene-Reduction of alpha , beta-Unsaturated Compounds by F 420 -Dependent Oxidoreductases A Enzymes from Mycobacterium smegmatis . Authors: Kang, S.W. / Antoney, J. / Frkic, R.L. / Lupton, D.W. / Speight, R. / Scott, C. / Jackson, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 447.5 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y9iS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15462.487 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.3 M potassium phosphate, 0.7 M sodium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.35→45.54 Å / Num. obs: 40092 / % possible obs: 100 % / Redundancy: 76.5 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.135 / Net I/σ(I): 23.8 / Num. measured all: 3067306 / Scaling rejects: 2 | |||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4Y9I Resolution: 1.35→45.54 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.84 Å2 / Biso mean: 31.1122 Å2 / Biso min: 15.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→45.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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