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Yorodumi- PDB-1mxr: High resolution structure of Ribonucleotide reductase R2 from E. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mxr | ||||||
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Title | High resolution structure of Ribonucleotide reductase R2 from E. coli in its oxidised (Met) form | ||||||
Components | Ribonucleotide reductase R2 | ||||||
Keywords | OXIDOREDUCTASE / Radical protein / di iron | ||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Andersson, M.A. / Hogbom, M. / Nordlund, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2003 Title: Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-A x-ray data. Authors: Hogbom, M. / Galander, M. / Andersson, M. / Kolberg, M. / Hofbauer, W. / Lassmann, G. / Nordlund, P. / Lendzian, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mxr.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mxr.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/1mxr ftp://data.pdbj.org/pub/pdb/validation_reports/mx/1mxr | HTTPS FTP |
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-Related structure data
Related structure data | 1xikS 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
#1: Protein | Mass: 43426.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pTB2 / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-HG / #4: Chemical | ChemComp-GOL / | #5: 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: 2.06 Å3/Da / Density % sol: 40.41 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, MES, NaCl, EMTS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Nordlund, P. (1989) FEBS Lett., 258, 251. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.87961 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 1999 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87961 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→40 Å / Num. all: 123371 / Num. obs: 123371 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.064 |
Reflection shell | Resolution: 1.42→1.47 Å / Rmerge(I) obs: 0.288 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 603231 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 91.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: reduced e. coli RNR R2 (1XIK) Resolution: 1.42→36.83 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.6682 Å2 / ksol: 0.375864 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.42→36.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.51 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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