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Yorodumi- PDB-4erm: Crystal structure of the dATP inhibited E. coli class Ia ribonucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4erm | ||||||
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Title | Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex at 4 Angstroms resolution | ||||||
Components | (Ribonucleoside-diphosphate reductase 1 subunit ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / protein-protein complex / alpha/beta barrel / atp cone / di-iron center / RNR alpha / RNR beta / thioredoxin / Ribonucleotide reduction / Cytosol | ||||||
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 / iron ion binding / ATP 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 / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.95 Å | ||||||
Authors | Zimanyi, C.M. / Drennan, C.L. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Authors: Christina M Zimanyi / Nozomi Ando / Edward J Brignole / Francisco J Asturias / Joanne Stubbe / Catherine L Drennan / Abstract: Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that ...Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4erm.cif.gz | 776.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4erm.ent.gz | 655.1 KB | Display | PDB format |
PDBx/mmJSON format | 4erm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4erm_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 4erm_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 4erm_validation.xml.gz | 180.5 KB | Display | |
Data in CIF | 4erm_validation.cif.gz | 234.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4erm ftp://data.pdbj.org/pub/pdb/validation_reports/er/4erm | HTTPS FTP |
-Related structure data
Related structure data | 5430C 5431C 5432C 5433C 5434C 5435C 5436C 5437C 4erpC 3uusS 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
-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 K-12 (bacteria) / Strain: K12 / Gene: b2234, dnaF, JW2228, nrdA / 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 K-12 (bacteria) / Strain: K12 / Gene: b2235, ftsB, JW2229, nrdB / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase |
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-Non-polymers , 5 types, 28 molecules
#3: Chemical | ChemComp-DTP / #4: Chemical | ChemComp-DAT / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-FEO / #7: 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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Precipitant conditions: 10% PEG 3350, 0.1 M MOPS pH 7.5, 0.2 M Magnesium Acetate, 0.025 M Magnesium Chloride, 0.006 M n-Nonyl-beta-D-maltopyranoside, and 5% glycerol. Mixed 1:1 with protein. ...Details: Precipitant conditions: 10% PEG 3350, 0.1 M MOPS pH 7.5, 0.2 M Magnesium Acetate, 0.025 M Magnesium Chloride, 0.006 M n-Nonyl-beta-D-maltopyranoside, and 5% glycerol. Mixed 1:1 with protein., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3.95→30 Å / Num. all: 55058 / Num. obs: 53173 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.161 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.95→4.09 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 5306 / Rsym value: 0.457 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3UUS Resolution: 3.95→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.95→4.09 Å
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