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Open data
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Basic information
Entry | Database: PDB / ID: 6t87 | ||||||||||||
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Title | Urocanate reductase in complex with urocanate | ||||||||||||
![]() | Urocanate reductase | ||||||||||||
![]() | OXIDOREDUCTASE / urocanate reductase / bacterial enzyme | ||||||||||||
Function / homology | ![]() urocanate reductase / steroid metabolic process / FMN binding / oxidoreductase activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Venskutonyte, R. / Lindkvist-Petersson, K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production. Authors: Venskutonyte, R. / Koh, A. / Stenstrom, O. / Khan, M.T. / Lundqvist, A. / Akke, M. / Backhed, F. / Lindkvist-Petersson, 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 | ![]() | 292.3 KB | Display | ![]() |
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PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 901.3 KB | Display | ![]() |
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Full document | ![]() | 902.3 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t85C ![]() 6t86C ![]() 6t88C ![]() 1d4cS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49984.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Truncated UrdA, construct comprising residues 130-582 and a C-terminal 6xHis tag. Source: (gene. exp.) ![]() Strain: MR-1 / Gene: urdA, SO_4620 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 605 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/URO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/URO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||||||
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#3: Chemical | ChemComp-URO / ( | ||||||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 27 % PEG8000 0.3 M (NH4)2SO4 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 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: 1.56→45.23 Å / Num. obs: 83093 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.021 / Rrim(I) all: 0.094 / Net I/σ(I): 20.2 / Num. measured all: 1681179 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1D4C Resolution: 1.56→45.227 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.54 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 105.46 Å2 / Biso mean: 26.4714 Å2 / Biso min: 14.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→45.227 Å
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