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- PDB-5udg: Mutant E97Q crystal structure of Bacillus subtilis QueF with a di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5udg | ||||||
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Title | Mutant E97Q crystal structure of Bacillus subtilis QueF with a disulfide Cys 55-99 | ||||||
![]() | NADPH-dependent 7-cyano-7-deazaguanine reductase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohammad, A. / Kiani, M.K. / Iwata-Reuyl, D. / Stec, B. / Swairjo, M. | ||||||
![]() | ![]() Title: Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide. Authors: Mohammad, A. / Bon Ramos, A. / Lee, B.W. / Cohen, S.W. / Kiani, M.K. / Iwata-Reuyl, D. / Stec, B. / 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 | ![]() | 170.9 KB | Display | ![]() |
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PDB format | ![]() | 135.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4f8bS S: Starting model for refinement |
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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
#1: Protein | Mass: 17247.570 Da / Num. of mol.: 5 / Fragment: UNP resdiues 21-165 / Mutation: E97Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: queF, A9D36_18900, AX282_02560, B4122_4589, B4417_3799, BN2127_JRS11_03356, BN2127_JRS2_02117, BN2127_JRS6_01198, BN2127_JRS9_01727, SC09_Contig19orf00807 Production host: ![]() ![]() ![]() References: UniProt: A0A063X9I2, UniProt: O31678*PLUS, ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PGE / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: Rhomboidal |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein sample 4 mg/mL, in 50 mM Tris pH 7.5, 50 mM KCl, 1 mM MgCl2 and 1 mM (mercaptoethanol-BME) was mixed with reservoir solution (1:1 ratio) containing 19% PEG 550 monomethyl ether, 43 ...Details: Protein sample 4 mg/mL, in 50 mM Tris pH 7.5, 50 mM KCl, 1 mM MgCl2 and 1 mM (mercaptoethanol-BME) was mixed with reservoir solution (1:1 ratio) containing 19% PEG 550 monomethyl ether, 43 mM imidazole-Cl (pH 6.8), 53 mM imidazole (pH 8.2), 30 mM CaCl2, and 4% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→45.61 Å / Num. obs: 30298 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.83 / CC1/2: 0.75 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4F8B Resolution: 2.5→45.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.067 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.723 / ESU R Free: 0.355 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.938 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→45.61 Å
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Refine LS restraints |
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