[English] 日本語
Yorodumi- PDB-3uus: Crystal structure of the dATP inhibited E. coli class Ia ribonucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uus | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / 10 stranded alpha/beta barrel / dATP bound / di-iron | ||||||
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: 5.65 Å | ||||||
Authors | Zimanyi, C.M. / Drennan, C.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Authors: Ando, N. / Brignole, E.J. / Zimanyi, C.M. / Funk, M.A. / Yokoyama, K. / Asturias, F.J. / Stubbe, J. / Drennan, C.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3uus.cif.gz | 753.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3uus.ent.gz | 631.6 KB | Display | PDB format |
PDBx/mmJSON format | 3uus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uus_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3uus_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3uus_validation.xml.gz | 170.9 KB | Display | |
Data in CIF | 3uus_validation.cif.gz | 220.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/3uus ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uus | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 85877.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / 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 (E. coli) / Strain: K12 / Gene: b2235, ftsB, JW2229, nrdB / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #3: Chemical | ChemComp-DTP / #4: Chemical | ChemComp-FE / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10.8% PEG 3350, 0.18M magnesium acetate, 0.09M MOPS pH 7.5, 0.01M iron (III) chloride, 4.5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2010 |
Radiation | Monochromator: Double crystal, 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: 5.65→50 Å / Num. all: 19267 / Num. obs: 19134 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.074 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 5.65→5.85 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1871 / Rsym value: 0.599 / % possible all: 99.4 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2R1R and PDB entry 1MXR Resolution: 5.65→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.65→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|