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Yorodumi- PDB-2zlf: The Structural Basis for Peptidomimetic Inhibition of Eukaryotic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zlf | ||||||
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Title | The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / peptidomimetic inhibition eukaryotic ribonucleotide reductase / Allosteric enzyme / ATP-binding / Cytoplasm / DNA replication / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Xu, H. / Fairman, J.W. / Wijerathna, S.R. / LaMacchia, J. / Kreischer, N.R. / Helmbrecht, E. / Cooperman, B.S. / Dealwis, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: A Conformationally Flexible Pharmacophore Authors: Xu, H. / Fairman, J.W. / Wijerathna, S.R. / Kreischer, N.R. / LaMacchia, J. / Helmbrecht, E. / Cooperman, B.S. / Dealwis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zlf.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zlf.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zlf ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zlf | HTTPS FTP |
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-Related structure data
Related structure data | 2zlgC 2cvxS 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
#1: Protein | Mass: 99672.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PWJ751-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P21524, ribonucleoside-diphosphate reductase |
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#2: Protein/peptide | Mass: 827.878 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Hepes, 20-25% PEG 3350, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 24929 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rsym value: 0.081 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.589→2.656 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.459 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CVX Resolution: 2.59→49.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.868 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.936 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→49.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.589→2.656 Å / Total num. of bins used: 20
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