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Yorodumi- PDB-5cnu: Crystal structure of the dATP inhibited E. coli class Ia ribonucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cnu | ||||||||||||
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Title | Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to ADP and dGTP at 3.40 Angstroms resolution | ||||||||||||
Components | (Ribonucleoside-diphosphate reductase 1 subunit ...) x 2 | ||||||||||||
Keywords | OXIDOREDUCTASE / allostery / substrate specificity / ribonucleotide reductase / nucleotide metabolism | ||||||||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||||||||
Authors | Chen, P.Y.-T. / Zimanyi, C.M. / Funk, M.A. / Drennan, C.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2016 Title: Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli. Authors: Zimanyi, C.M. / Chen, P.Y. / Kang, G. / Funk, M.A. / Drennan, C.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cnu.cif.gz | 853.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cnu.ent.gz | 702.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cnu_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 5cnu_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 5cnu_validation.xml.gz | 141.1 KB | Display | |
Data in CIF | 5cnu_validation.cif.gz | 190.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/5cnu ftp://data.pdbj.org/pub/pdb/validation_reports/cn/5cnu | HTTPS FTP |
-Related structure data
Related structure data | 5cnsC 5cntC 5cnvC 4ermS C: citing same article (ref.) S: Starting model for refinement |
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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
-Ribonucleoside-diphosphate reductase 1 subunit ... , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 85877.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: nrdA, dnaF, b2234, JW2228 / Production host: Escherichia coli (E. coli) References: UniProt: P00452, ribonucleoside-diphosphate reductase #2: Protein | Mass: 43426.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase |
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-Non-polymers , 6 types, 118 molecules
#3: Chemical | ChemComp-DGT / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ADP / #6: Chemical | ChemComp-DAT / #7: Chemical | ChemComp-FEO / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% (w/v) PEG 3350, 100 mM MOPS pH 7.5, 300 mM Mg(CH3COO)2, 30 mM MgCl2, and 5% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→49.664 Å / Num. obs: 80047 / % possible obs: 93.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.127 / Net I/av σ(I): 8.1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.4 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ERM Resolution: 3.4→49.653 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→49.653 Å
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Refine LS restraints |
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LS refinement shell |
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