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- PDB-7ms8: Crystal structure of Y103F mutant of Cg10062 with a covalent inte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ms8 | ||||||
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Title | Crystal structure of Y103F mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid | ||||||
![]() | 4-oxalocrotonate tautomerase | ||||||
![]() | ISOMERASE / tautomerase | ||||||
Function / homology | Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / 4-oxalocrotonate tautomerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nayebi, G.H. / Geiger, J.H. / Draths, K. | ||||||
![]() | ![]() Title: Cg10062 Catalysis Forges a Link between Acetylenecarboxylic Acid and Bacterial Metabolism. Authors: Mathes Hewage, A. / Nayebi Gavgani, H. / Chi, D. / Qiu, B. / Geiger, J.H. / Draths, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.7 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.7 KB | Display | ![]() |
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Full document | ![]() | 757.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ms0SC ![]() 7ms1C ![]() 7ms3C ![]() 7ms9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 19022.250 Da / Num. of mol.: 1 / Mutation: Y103F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: APT58_00490, AUO95_07180, CS176_0056, FM102_14895, KaCgl_17770, KbCgl_30240 Production host: ![]() ![]() References: UniProt: A0A0S2T163, 2-hydroxymuconate tautomerase |
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#2: Chemical | ChemComp-3OH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.91 Å3/Da / Density % sol: 82.21 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM magnesium acetate tetrahydrate, 10% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.65 Å / Num. obs: 19222 / % possible obs: 99.84 % / Redundancy: 10.4 % / Biso Wilson estimate: 56.68 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 1895 / Rpim(I) all: 0.482 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7MS0 Resolution: 2.5→33.65 Å / SU ML: 0.3241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4747 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33.65 Å
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Refine LS restraints |
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LS refinement shell |
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