+Open data
-Basic information
Entry | Database: PDB / ID: 6t85 | ||||||||||||
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Title | Urocanate reductase in complex with ADP | ||||||||||||
Components | Urocanate reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / urocanate reductase / bacterial enzyme | ||||||||||||
Function / homology | Function and homology information urocanate reductase / steroid metabolic process / FMN binding / oxidoreductase activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å | ||||||||||||
Authors | Venskutonyte, R. / Lindkvist-Petersson, K. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Nat Commun / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t85.cif.gz | 316.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t85.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 6t85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t85_validation.pdf.gz | 696.8 KB | Display | wwPDB validaton report |
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Full document | 6t85_full_validation.pdf.gz | 696.8 KB | Display | |
Data in XML | 6t85_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 6t85_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t85 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t85 | HTTPS FTP |
-Related structure data
Related structure data | 6t86C 6t87C 6t88C 1d4cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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.) Shewanella oneidensis (strain MR-1) (bacteria) Strain: MR-1 / Gene: urdA, SO_4620 / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CVD0, urocanate reductase | ||||||
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#2: Chemical | ChemComp-ADP / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 % PEG4000 0.1 M MgCl2 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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→63.19 Å / Num. obs: 198264 / % possible obs: 98.6 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.036 / Rrim(I) all: 0.111 / Net I/σ(I): 9.5 / Num. measured all: 1753417 / Scaling rejects: 452 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D4C Resolution: 1.1→63.189 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 60.89 Å2 / Biso mean: 14.9925 Å2 / Biso min: 5.76 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→63.189 Å
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