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Yorodumi- PDB-1yfd: Crystal structure of the Y122H mutant of ribonucleotide reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yfd | ||||||
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Title | Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli | ||||||
Components | Ribonucleoside-diphosphate reductase 1 beta chain | ||||||
Keywords | OXIDOREDUCTASE / di-iron center | ||||||
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 / iron ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kolberg, M. / Logan, D.T. / Bleifuss, G. / Poetsch, S. / Sjoeberg, B.M. / Graeslund, A. / Lubitz, W. / Lassmann, G. / Lendzian, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies Authors: Kolberg, M. / Logan, D.T. / Bleifuss, G. / Poetsch, S. / Sjoeberg, B.M. / Graeslund, A. / Lubitz, W. / Lassmann, G. / Lendzian, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfd.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfd.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yfd_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 1yfd_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 1yfd_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1yfd_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfd ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfd | HTTPS FTP |
-Related structure data
Related structure data | 1pfrS 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: 43401.836 Da / Num. of mol.: 2 / Mutation: Y122H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: Expression system used in combination with a second plasmid, pGP1-2, for overexpression of R2-Y122H using heat induction of the T7 RNA polymerase Gene: nrdB, ftsB / Plasmid: pTB2-Y122H / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009 References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-HG / #3: Chemical | #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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, 0.1M MES, 0.4M NACL, 1mM EMTS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 27, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.6 Å / Num. obs: 57178 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.084 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.233 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PFR Resolution: 1.9→19.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.493 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STEREOCHEMICAL DISTORTIONS reported in remark 500 ARE DUE TO THE PROXIMITY OF THESE RESIDUES TO STRONGLY DIFFRACTING MERCURY IONS IN THE CRYSTAL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.662 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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