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Yorodumi- PDB-2r2f: RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r2f | ||||||
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Title | RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM (OXIDIZED) | ||||||
Components | PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN) | ||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / NUCLEOTIDE METABOLISM | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å | ||||||
Authors | Eklund, H. / Eriksson, M. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms. Authors: Eriksson, M. / Jordan, A. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r2f.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r2f.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r2f_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2r2f_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 2r2f_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 2r2f_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/2r2f ftp://data.pdbj.org/pub/pdb/validation_reports/r2/2r2f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.807926, 0.583994, -0.078779), Vector: |
-Components
#1: Protein | Mass: 36262.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PET24A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P17424, ribonucleoside-diphosphate reductase #2: Chemical | #3: 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: 2.77 Å3/Da / Density % sol: 55.56 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8373 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 36792 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rsym value: 0.066 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3 % / Rsym value: 0.253 / % possible all: 99.5 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.253 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 42.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |