Photoproduction of charged pions on neutrons

Ramachandran, G.; Keshavamurthy, R. S.; Murthy, M. V. N.

doi:10.1088/0305-4616/7/7/522

Cited by 6 publications

(6 citation statements)

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“…The crystallographic R-factor of the refined model is 21.6%, using all 22653 observed reflections between 8.0 and 2.8 A resolution. From a Luzzati plot (Luzzati, 1952) angles fall in or very close to the 'allowed' regions (see Ramachandran et al, 1963). The quality of the model before and after refinement is illustrated in Figure 1 by a real space R-factor plot (Brand6n and Jones, 1990).…”

Section: Refinementmentioning

confidence: 99%

Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

et al. 1991

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P1 nuclease from Penicillium citrinum is a zinc dependent glyco‐enzyme consisting of 270 amino acid residues which cleaves single‐stranded RNA and DNA into 5′‐mononucleotides. The X‐ray structure of a tetragonal crystal form of the enzyme with two molecules per asymmetric unit has been solved at 3.3 and refined at 2.8 A resolution to a crystallographic R‐factor of 21.6%. The current model consists of 269 amino acid residues, three Zn ions and two N‐acetyl glucosamines per subunit. The enzyme is folded very similarly to phospholipase C from Bacillus cereus, with 56% of the structure displaying an alpha‐helical conformation. The three Zn ions are located at the bottom of a cleft and appear to be rather inaccessible for any phosphate group in double‐stranded RNA or DNA substrates. A crystal soaking experiment with a dinucleotide gives clear evidence for two mononucleotide binding sites separated by approximately 20 A. One site shows binding of the phosphate group to one of the zinc ions. At both sites there is a hydrophobic binding pocket for the base, but no direct interaction between the protein and the deoxyribose. A cleavage mechanism is proposed involving nucleophilic attack by a Zn activated water molecule.

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Section: Refinementmentioning

confidence: 99%

Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

et al. 1991

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“…The ®nal model with 1400 non-H protein atoms, 176 solvent water molecules and ®ve sulfate ions shows good stereochemistry. The main-chain dihedral angles (9, 2) are within the allowed limits (Morris et al, 1992) in the Ramachandran plot (Ramachandran et al, 1963;Fig. 2) and the results from PROCHECK (Laskowski et al, 1993) show that around 134 residues (88.7%) are in the core region, 16 residues (10.6%) are in the allowed region and only one residue (0.6%) is in the generously allowed region of the plot.…”

Section: Quality Of the Modelmentioning

confidence: 63%

Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 Å resolution

Ravichandran

Sen

Chakrabarti

et al. 1999

Acta Crystallogr D Biol Cryst

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The crystal structure of a Kunitz-type double-headed alpha--chymotrypsin inhibitor from winged bean seeds has been refined at 2.13 A resolution using data collected from cryo-cooled (90 K) crystals which belong to the hexagonal space group P6(1)22 with unit-cell parameters a = b = 60.84, c = 207.91 A. The volume of the unit cell is reduced by 5.3% on cooling. The refinement converged to an R value of 20.0% (R(free) = 25.8%) for 11100 unique reflections and the model shows good stereochemistry, with r.m.s. deviations from ideal values for bond lengths and bond angles of 0.011 A and 1.4 degrees, respectively. The structural architecture of the protein consists of 12 antiparallel beta-strands joined in the form of a characteristic beta-trefoil fold, with the two reactive-site regions, Asn38-Leu43 and Gln63-Phe68, situated on two external loops. Although the overall protein fold is the same as that of the room-temperature model, some conformational changes are observed in the loop regions and in the side chains of a few surface residues. A total of 176 ordered water molecules and five sulfate ions are included in the model.

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“…There is no available a x-ray structure for XIIMe peptide; therefore, a XIIMe initial theoretical model was built. The and ␤-helix dihedral angle values from the literature 8,33 were applied to an extended D,L alternating polynorleucine chain, and used for the generation of the XIIMe empirical model. Conformational energy calculations have shown that the ␤-helix with 4.4, 6.3, and 8.3 residues per turn are stable structures.…”

Section: Methodsmentioning

confidence: 99%

Solution NMR structure of a D,L‐alternating oligonorleucine as a model of β‐helix

et al. 2001

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beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR experimental data and theoretical calculations clearly indicate that the XIIMe adopts a single beta(4.4)-helix-type conformation in nonpolar solvents.

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Photoproduction of charged pions on neutrons

Cited by 6 publications

References 0 publications

Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 Å resolution

Solution NMR structure of a D,L‐alternating oligonorleucine as a model of β‐helix

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