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- PDB-7mgo: Crystal structure of F501H variant of 2-ketopropyl coenzyme M oxi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mgo | ||||||
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Title | Crystal structure of F501H variant of 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) from Xanthobacter autotrophicus | ||||||
![]() | 2-oxopropyl-CoM reductase, carboxylating | ||||||
![]() | OXIDOREDUCTASE / carboxylation / oxidation-reduction / carbon dioxide fixation / carbon-carbon bond / anion-binding / kinetics | ||||||
Function / homology | ![]() 2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process / NAD(P)H dehydrogenase (quinone) activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prussia, G. / Zadvornyy, O.A. / Peters, J.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage. Authors: Prussia, G.A. / Shisler, K.A. / Zadvornyy, O.A. / Streit, B.R. / DuBois, J.L. / Peters, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421 KB | Display | ![]() |
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PDB format | ![]() | 340.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 65.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mgnC ![]() 2c3cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57405.316 Da / Num. of mol.: 2 / Mutation: F501H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-1158 / Py2 / Gene: xecC, Xaut_4867 Production host: ![]() ![]() References: UniProt: Q56839, 2-oxopropyl-CoM reductase (carboxylating) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.17 M ammonium acetate, 0.085 M trisodium citrate pH 5.6, 27% PEG 4,000, and 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9884 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→39.19 Å / Num. obs: 87767 / % possible obs: 95.9 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Rmerge(I) obs: 0.705 / Num. unique obs: 10655 / CC1/2: 0.685 / Rpim(I) all: 0.461 / Rrim(I) all: 0.848 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2c3c Resolution: 1.85→39.19 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.19 Å
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Refine LS restraints |
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LS refinement shell |
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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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