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Yorodumi- PDB-6lkm: Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lkm | ||||||
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Title | Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide | ||||||
Components | Ribonucleoside-diphosphate reductase large subunitRibonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / mitochondrial DNA replication / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cell projection / male gonad development / disordered domain specific binding / retina development in camera-type eye / nuclear envelope / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Miyahara, S. / Chong, K.T. / Suzuki, T. | ||||||
Citation | Journal: To be published Title: TAS1553, a novel small molecule ribonucleotide reductase (RNR) subunit interaction inhibitor, displays remarkable anti-tumor activity Authors: Miyahara, S. / Hara, S. / Chong, K.T. / Suzuki, T. / Ogino, Y. / Hoshino, T. / Tsukioka, S. / Yano, W. / Suzuki, M. / Otsu, Y. / Yonekura, T. / Ito, S. / Terasaka, M. / Suzuki, T. / Hashimoto, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lkm.cif.gz | 276.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lkm.ent.gz | 219.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lkm ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lkm | HTTPS FTP |
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-Related structure data
Related structure data | 6l3rC 6l7lC 2wghS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 76189.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRM1, RR1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P23921, ribonucleoside-diphosphate reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.68 Å3/Da / Density % sol: 54.07 % / Mosaicity: 0.56 ° |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate buffer, PEG3350, Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.997 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→110.617 Å / Num. obs: 52639 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.086 / Rsym value: 0.071 / Net I/av σ(I): 7.6 / Net I/σ(I): 10.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WGH Resolution: 2.55→110.617 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.404 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.665 / ESU R Free: 0.333 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.7 Å2 / Biso mean: 51.036 Å2 / Biso min: 22.26 Å2
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Refinement step | Cycle: final / Resolution: 2.55→110.617 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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