Citations in PubMed

Primary Citation PubMed: 24150947 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 1

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP?Mg2+ and 5'-OH oligonucleotide and a product complex with GDP?Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.

(2014) Nucleic Acids Res 42

PubMed: 24150947 | PubMedCentral: PMC3902929 | DOI: 10.1093/nar/gkt936

ACCESSION NUMBERS The coordinates for the Michaelis complex and product complex have been deposited in the RCSB protein structure database (pdb ID codes 4MDF and 4MDE).

Crystallographic data and refinement statistics Cth Pnk•GTP•Mg 2+ • HO DNA Cth Pnk•GDP•Mg 2+ •pDNA Space group P2 1 2 1 2 1 P2 1 2 1 2 1 Unit cell dimensions (Å) @ 130 K a = 53.0 a = 54.4 b = 72.8 b = 73.1 c = 119.5 c = 119.0 Diffraction data quality     Resolution (Å) 53.0–1.73 (1.76–1.73) 46.2–1.8 (1.9–1.8)     Radiation source NSLS X25 NSLS X25     Wavelength 1.10 Å 1.10 Å     Processing software Mosflm/Scala Mosflm/Scala     R sym a , % 8.4 (38.7) 4.5 (19.8)     Unique reflections 49 311 (2645) 43 723 (6304)     Mean redundancy 11.9 (7.4) 3.0 (3.0)     Completeness, % 100.0 (99.2) 97.8 (97.6)     Mean I/σI 20.1 (4.7) 13.6 (4.7) Phasing statistics     Phasing method Phenix AutoMR     Resolution (Å) 53.0–2.0     Signal to noise b RFZ = 27.6, TFZ = 38.2 Refinement and model statistics ( F > 0)     Resolution (Å) 48.5–1.73 (1.75–1.73) 41.0–1.8 (1.82–1.80)     Completeness, % 99.5 (97.2) 97.3 (98.0)      R free c / R work , % 19.6/16.3 (27.7/22.3) 20.6/16.4 (27.1/22.3)     RMSD bonds/angles 0.006 Å/1.13° 0.006 Å/1.09°     Protomers/ASU 2 2     Ramachandran plot 99.4% favored, no outliers 99.1% favored, no outliers  B-factors, Å 2         Overall/Wilson 21.3/17.8 21.8/20.0     PDB ID 4MDF 4MDE Model contents     Protein residues 342 342     Heteroatoms 2 GTP, 2 Mg 2+ , 1 citrate, 2 oligonucleotides 2 GDP, 2 Mg 2+ , 2 oligonucleotides     Water 395 440 Standard definitions are used for all parameters.

Publication Year: 2014