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Open data
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Basic information
Entry | Database: PDB / ID: 2xo4 | ||||||
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Title | RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI | ||||||
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![]() | OXIDOREDUCTASE / NUCLEOTIDE-BINDING / ALTERNATIVE INITIATION / DNA REPLICATION / ALLOSTERIC ENZYME | ||||||
Function / homology | ![]() 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 / protein folding chaperone / iron ion binding / ATP binding ...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 / protein folding chaperone / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J. | ||||||
![]() | ![]() Title: Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine- Substituted Escherichia Coli Ribonucleotide Reductases. Authors: Minnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J. #1: ![]() Title: Structure of Ribonucleotide Reductase Protein R1 Authors: Uhlin, U. / Eklund, H. #2: ![]() Title: Binding of Allosteric Effectors to Ribonucleotide Reductase Protein R1: Reduction of Active-Site Cysteines Promotes Substrate Binding Authors: Eriksson, M. / Uhlin, U. / Ramaswamy, S. / Ekberg, M. / Regnstrom, K. / Sjoberg, B.M. / Eklund, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 460.6 KB | Display | ![]() |
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PDB format | ![]() | 378.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xo5C ![]() 2x0xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 85892.102 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-761 Source method: isolated from a genetically manipulated source Details: SITE SPECIFIC INCORPORATION OF 3-AMINOTYROSINE AT POSITION 730 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00452, ribonucleoside-diphosphate reductase #2: Protein/peptide | Mass: 2271.392 Da / Num. of mol.: 4 Fragment: RIBONUCLEOTIDE REDUCTASE R2-PEPTIDE, RESIDUES 357-376 Source method: obtained synthetically / Source: (synth.) ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6 Details: LITHIUM SULPHATE 1.5M, SODIUM CHLORIDE BUFFER PH 6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→84.21 Å / Num. obs: 112261 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 4.47 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.5→2.52 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.94 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X0X Resolution: 2.5→169.031 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.084 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.376 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT Y731 AND N733 HAVE TWO POSITIONS. THE SECOND POSITION FOR THESE RESIDUES ARE BUILT IN MOLECULE C. THE 11-16 C-TERMINAL RESIDUES OF THE R2 PEPTIDE, CHAINS D, E, F BIND AT THE R2 BINDING-SITE OF THE R1 MOLECULES, CHAINS A, B, C. THE THREE N-TERMINAL RESIDUES, UNIQUE CHAIN P, ARE SITUATED BETWEEN MOL A AND C. THIS LATTER BINDING HAS NO KNOWN BIOLOGICAL RELEVANCE BUT IS ESSENTIAL FOR CRYSTAL LATTICE FORMATION. WATERS CLOSE TO SER 625 MAY REPRESENT A SULPHATE ION.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.867 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→169.031 Å
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Refine LS restraints |
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