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Yorodumi- PDB-1pj1: RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F SOAKED WITH FERROUS IONS AT PH 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pj1 | ||||||
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Title | RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F SOAKED WITH FERROUS IONS AT PH 5 | ||||||
Components | Ribonucleoside-diphosphate reductase 1 beta chain | ||||||
Keywords | OXIDOREDUCTASE / Four helix bundle / diferrous cluster | ||||||
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: 1.95 Å | ||||||
Authors | Voegtli, W.C. / Sommerhalter, M. / Saleh, L. / Baldwin, J. / Bollinger Jr., J.M. / Rosenzweig, A.C. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2. Authors: Voegtli, W.C. / Sommerhalter, M. / Saleh, L. / Baldwin, J. / Bollinger Jr., J.M. / Rosenzweig, A.C. | ||||||
History |
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Remark 999 | SEQUENCE THE CONFLICTS ARE DUE TO A MODELLING ERROR IN THE INITIAL MODEL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pj1.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pj1.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pj1 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pj1 | HTTPS FTP |
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-Related structure data
Related structure data | 1piyC 1pizC 1pj0C 1pm2C 1r65C 1piuS 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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Details | Tetramer of two alpha and two beta subunits |
-Components
#1: Protein | Mass: 43387.824 Da / Num. of mol.: 2 / Mutation: D84E, W48F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RIR2 / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-HG / #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: 2.06 Å3/Da / Density % sol: 40.32 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 4000, 200mM NaCl, 50mM MES, 0.3% dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 52978 / Num. obs: 51480 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 16.8 Å2 |
Reflection shell | Resolution: 1.95→2.07 Å / % possible all: 93.7 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 52866 / % possible obs: 99.5 % / Num. measured all: 393987 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PIU Resolution: 1.95→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 713916.89 / Data cutoff high rms absF: 713916.89 / Data cutoff low absF: 0 / 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: 47.2515 Å2 / ksol: 0.385052 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 4.8 % / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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