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Yorodumi- PDB-2xap: Ribonucleotide reductase Y731NO2Y modified R1 subunit of E. coli ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xap | |||||||||
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Title | Ribonucleotide reductase Y731NO2Y modified R1 subunit of E. coli to 2. 1 A resolution | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / DNA REPLICATION / ALLOSTERIC ENZYME / NUCLEOTIDE-BINDING | |||||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / 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 / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Yokoyama, K. / Uhlin, U. / Stubbe, J. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Site-Specific Incorporation of 3-Nitrotyrosine as a Probe of Pk(A) Perturbation of Redox-Active Tyrosines in Ribonucleotide Reductase. Authors: Yokoyama, K. / Uhlin, U. / Stubbe, J. #1: Journal: Nature / Year: 1994 Title: Structure of Ribonucleotide Reductase Protein R1. Authors: Uhlin, U. / Eklund, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xap.cif.gz | 465.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xap.ent.gz | 381.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xap_validation.pdf.gz | 483.4 KB | Display | wwPDB validaton report |
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Full document | 2xap_full_validation.pdf.gz | 506.3 KB | Display | |
Data in XML | 2xap_validation.xml.gz | 88.3 KB | Display | |
Data in CIF | 2xap_validation.cif.gz | 129.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xap ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xap | HTTPS FTP |
-Related structure data
Related structure data | 2x0xSC 2xakC 2xavC 2xawC 2xaxC 2xayC 2xazC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 85922.086 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-761 Source method: isolated from a genetically manipulated source Details: SITE SPECIFIC INCORPORATION OF 3-NITROTYROSINE AT POSITION 731 Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PBADMYCHISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 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.) ESCHERICHIA COLI (E. coli) / References: UniProt: P69924 #3: Water | ChemComp-HOH / | Sequence details | SITE SPECIFIC INCORPORAT | |
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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: 3.02 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.99 Å / Num. obs: 177593 / % possible obs: 95.2 % / Observed criterion σ(I): -3.7 / Redundancy: 8.17 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.15 |
Reflection shell | Resolution: 2.1→2.12 Å / Redundancy: 8.05 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.34 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X0X Resolution: 2.1→169.031 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.239 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.195 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 268-273 ARE DISORDERED. THE 16 C-TERMINAL RESIDUES OF THE BIND AT THE R2 BINDING-SITE OF THE R1 MOLECULES (CHAINS A, B, C). ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 268-273 ARE DISORDERED. THE 16 C-TERMINAL RESIDUES OF THE BIND AT THE R2 BINDING-SITE OF THE R1 MOLECULES (CHAINS A, B, C). (UNIQUE CHAIN P) ARE SITUATED BETWEEN MOL A AND C. THIS LATTER BI NO KNOWN BIOLOGICAL RELEVANCE BUT IS NEEDED FOR CRYSTAL LATTICE FORMATION. WATERS CLOSE TO SER 625 MAY REPRESENT A SULPHAT
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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: 35.061 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→169.031 Å
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