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- PDB-7u5a: Crystal structure of queuine salvage enzyme DUF2419 mutant K199C,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u5a | |||||||||
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Title | Crystal structure of queuine salvage enzyme DUF2419 mutant K199C, complexed with queuosine | |||||||||
![]() | Queuine salvage enzyme DUF2419 | |||||||||
![]() | HYDROLASE / 7-deazaguanine salvage / queuosine / tRNA modification | |||||||||
Function / homology | Queuosine salvage protein family / Queuosine salvage protein / tRNA-guanine transglycosylation / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / MALONATE ION / 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 | ![]() | 283.4 KB | Display | ![]() |
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PDB format | ![]() | 229.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 962.7 KB | Display | ![]() |
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Full document | ![]() | 968 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u07SC ![]() 7u1oC ![]() 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: 37162.648 Da / Num. of mol.: 2 / Mutation: K199C 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 | ChemComp-MLI / | #4: 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: 3.1 Å3/Da / Density % sol: 60.37 % / Description: Long, thin clustered crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / 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: Jun 26, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→37.65 Å / Num. obs: 32478 / % possible obs: 100 % / Redundancy: 26.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.057 / Rrim(I) all: 0.296 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7U07 Resolution: 2.5→37.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2017 / WRfactor Rwork: 0.1512 / FOM work R set: 0.8394 / SU B: 18.49 / SU ML: 0.167 / SU Rfree: 0.2155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / 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: 148.81 Å2 / Biso mean: 54.753 Å2 / Biso min: 31.88 Å2
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Refinement step | Cycle: final / Resolution: 2.5→37.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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