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Yorodumi- PDB-6cgl: X-ray crystal structure of Bacillus subtilis ribonucleotide reduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cgl | |||||||||
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Title | X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound as-isolated (pH 4) | |||||||||
Components | Ribonucleoside-diphosphate reductaseRibonucleotide reductase | |||||||||
Keywords | OXIDOREDUCTASE / ribonucleotide reductase / allostery / nucleotide metabolism / dAMP | |||||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / ATP binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Maggiolo, A.O. / Boal, A.K. | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP. Authors: Parker, M.J. / Maggiolo, A.O. / Thomas, W.C. / Kim, A. / Meisburger, S.P. / Ando, N. / Boal, A.K. / Stubbe, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cgl.cif.gz | 276.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cgl.ent.gz | 222.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/6cgl ftp://data.pdbj.org/pub/pdb/validation_reports/cg/6cgl | HTTPS FTP |
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-Related structure data
Related structure data | 6cgmC 6cgnC 1pemS 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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Unit cell |
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-Components
#1: Protein | Mass: 80791.469 Da / Num. of mol.: 2 / Fragment: \cf2 \cf0 Source method: isolated from a genetically manipulated source Details: tag removed for crystallization / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3413, CFD21_09965 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A162Q3J9, UniProt: P50620*PLUS, ribonucleoside-diphosphate reductase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 3.66 Å3/Da / Density % sol: 66.39 % / Mosaicity: 0.339 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M citric acid (pH 4.0), 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 37370 / % possible obs: 98.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.092 / Rrim(I) all: 0.224 / Χ2: 1.015 / Net I/σ(I): 3.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PEM Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.819 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 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: 142.68 Å2 / Biso mean: 74.388 Å2 / Biso min: 17.26 Å2
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Refinement step | Cycle: final / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.201→3.284 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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