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Yorodumi- PDB-6ebp: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ebp | ||||||
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Title | Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form | ||||||
Components | Ribonucleoside-diphosphate reductase, beta subunitRibonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / post-translational modification / PTM / DOPA / radical | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane Similarity search - Function | ||||||
Biological species | Aerococcus urinae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å | ||||||
Authors | Palowitch, G.M. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical. Authors: Blaesi, E.J. / Palowitch, G.M. / Hu, K. / Kim, A.J. / Rose, H.R. / Alapati, R. / Lougee, M.G. / Kim, H.J. / Taguchi, A.T. / Tan, K.O. / Laremore, T.N. / Griffin, R.G. / Krebs, C. / Matthews, ...Authors: Blaesi, E.J. / Palowitch, G.M. / Hu, K. / Kim, A.J. / Rose, H.R. / Alapati, R. / Lougee, M.G. / Kim, H.J. / Taguchi, A.T. / Tan, K.O. / Laremore, T.N. / Griffin, R.G. / Krebs, C. / Matthews, M.L. / Silakov, A. / Bollinger Jr., J.M. / Allen, B.D. / Boal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ebp.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ebp.ent.gz | 214.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ebp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6ebp ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6ebp | HTTPS FTP |
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-Related structure data
Related structure data | 6eboSC 6ebqC 6ebzC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40682.383 Da / Num. of mol.: 4 / Mutation: Y123(DAH) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aerococcus urinae (strain ACS-120-V-Col10a) (bacteria) Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: F2I8X9, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THIS RESIDUE REPRESENTS | |
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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: 2.26 Å3/Da / Density % sol: 45.47 % / Mosaicity: 0.434 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% (w/v) PEG 4000, 0.3 M calcium chloride, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.59→50 Å / Num. obs: 193462 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.031 / Rrim(I) all: 0.086 / Χ2: 0.932 / Net I/σ(I): 8.5 / Num. measured all: 1407352 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 6EBO Resolution: 1.59→35.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.898 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.015 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 36.34 Å2 / Biso mean: 13.882 Å2 / Biso min: 5.79 Å2
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Refinement step | Cycle: final / Resolution: 1.59→35.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.586→1.627 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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