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Yorodumi- PDB-7ulc: Crystal structure of queuine salvage enzyme DUF2419 mutant D231N,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ulc | |||||||||
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Title | Crystal structure of queuine salvage enzyme DUF2419 mutant D231N, in complex with queuosine-5'-monophosphate | |||||||||
Components | Queuosine salvage protein DUF2419 | |||||||||
Keywords | HYDROLASE / 7-deazaguanine salvage / queuosine / tRNA modification | |||||||||
Function / homology | Queuosine salvage protein family / Queuosine salvage protein / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / Chem-56B / DI(HYDROXYETHYL)ETHER / Queuosine 5'-phosphate N-glycosylase/hydrolase Function and homology information | |||||||||
Biological species | Sphaerobacter thermophilus DSM 20745 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å | |||||||||
Authors | Hung, S.-H. / Swairjo, M.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ulc.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ulc.ent.gz | 229 KB | Display | PDB format |
PDBx/mmJSON format | 7ulc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ulc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ulc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ulc_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 7ulc_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ulc ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ulc | HTTPS FTP |
-Related structure data
Related structure data | 7u07SC 7u1oC 7u5aC 7u91C 7ugkC 7uk3C 8dl3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 37187.699 Da / Num. of mol.: 2 / Mutation: D231N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria) Strain: DSM 20745 / S 6022 / Gene: Sthe_2331 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: D1C7A6 #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.95 % / 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→50 Å / Num. obs: 62834 / % possible obs: 99.9 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.043 / Rrim(I) all: 0.179 / Χ2: 0.986 / Net I/σ(I): 4.5 / Num. measured all: 1056419 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7U07 Resolution: 1.99→47.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1715 / WRfactor Rwork: 0.1437 / FOM work R set: 0.9153 / SU B: 6.229 / SU ML: 0.073 / SU R Cruickshank DPI: 0.3231 / SU Rfree: 0.1141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.114 / 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: 100.75 Å2 / Biso mean: 32.533 Å2 / Biso min: 13.86 Å2
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Refinement step | Cycle: final / Resolution: 1.99→47.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.991→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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