+Open data
-Basic information
Entry | Database: PDB / ID: 1xsm | ||||||
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Title | PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE FROM MOUSE | ||||||
Components | RIBONUCLEOTIDE REDUCTASE R2 | ||||||
Keywords | OXIDOREDUCTASE / DNA REPLICATION / IRON | ||||||
Function / homology | Function and homology information deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / blastocyst development ...deoxyribonucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein heterotetramerization / blastocyst development / positive regulation of G1/S transition of mitotic cell cycle / ferric iron binding / nuclear envelope / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kauppi, B. / Nielsen, B.N. / Ramaswamy, S. / Kjoller-Larsen, I. / Thelander, M. / Thelander, L. / Eklund, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: The three-dimensional structure of mammalian ribonucleotide reductase protein R2 reveals a more-accessible iron-radical site than Escherichia coli R2. Authors: Kauppi, B. / Nielsen, B.B. / Ramaswamy, S. / Larsen, I.K. / Thelander, M. / Thelander, L. / Eklund, H. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 Authors: Nordlund, P. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xsm.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xsm.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/1xsm ftp://data.pdbj.org/pub/pdb/validation_reports/xs/1xsm | HTTPS FTP |
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-Related structure data
Related structure data | 1ribS 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: 45149.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: T7-RNA POLYMERASE / Gene: NRDD / Plasmid: PET / Gene (production host): NRDD / Production host: Escherichia coli (E. coli) References: UniProt: P11157, ribonucleoside-diphosphate reductase |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 9 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: 1.0-1.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.7, 0-4% PEG4000. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Nielsen, B.B., (1995) FEBS Letters, 373, 310. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 17131 / % possible obs: 95.87 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.29→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.283 / % possible all: 70.9 |
Reflection | *PLUS % possible obs: 95.8 % / Num. measured all: 144719 |
Reflection shell | *PLUS % possible obs: 70.9 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RIB Resolution: 2.3→25 Å / σ(F): 0
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Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 28.6 |