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- PDB-7u1o: Crystal structure of queuine salvage enzyme DUF2419 complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u1o | |||||||||
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Title | Crystal structure of queuine salvage enzyme DUF2419 complexed with queuosine | |||||||||
![]() | Queuine salvage enzyme DUF2419 | |||||||||
![]() | HYDROLASE / 7-deazaguanine salvage / queuosine / tRNA modification | |||||||||
Function / homology | Queuosine salvage protein family / Queuosine salvage protein / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / MALONATE ION / DI(HYDROXYETHYL)ETHER / Chem-QEO / Queuosine 5'-phosphate N-glycosylase/hydrolase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hung, S.-H. / Swairjo, M.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate. Authors: Hung, S.H. / Elliott, G.I. / Ramkumar, T.R. / Burtnyak, L. / McGrenaghan, C.J. / Alkuzweny, S. / Quaiyum, S. / Iwata-Reuyl, D. / Pan, X. / Green, B.D. / Kelly, V.P. / de Crecy-Lagard, V. / Swairjo, M.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.1 KB | Display | ![]() |
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PDB format | ![]() | 231.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u07SC ![]() 7u5aC ![]() 7u91C ![]() 7ugkC ![]() 7uk3C ![]() 7ulcC ![]() 8dl3C S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37188.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 20745 / S 6022 / Gene: Sthe_2331 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #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: 2.96 Å3/Da / Density % sol: 58.4 % / Description: Long, thin clustered crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001 |
-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: May 29, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→23 Å / Num. obs: 38007 / % possible obs: 100 % / Redundancy: 32.2 % / Rmerge(I) obs: 0.389 / Rpim(I) all: 0.069 / Rrim(I) all: 0.395 / Χ2: 1.059 / Net I/σ(I): 2.7 / Num. measured all: 1222832 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7U07 Resolution: 2.35→22.98 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1461 / WRfactor Rwork: 0.1093 / FOM work R set: 0.8419 / SU B: 14.108 / SU ML: 0.134 / SU Rfree: 0.1745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.83 Å2 / Biso mean: 39.108 Å2 / Biso min: 20.19 Å2
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Refinement step | Cycle: final / Resolution: 2.35→22.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.409 Å / Rfactor Rfree error: 0
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