The Crystals of acidic phospholipase A2 from the venom of Agkistrodon blomhoffii bre-vicaudus (i.e. Agkistrodon halys pallas) covalently modified with p-bromo-phenacylbromide wereobtained by the method of hanging drop...The Crystals of acidic phospholipase A2 from the venom of Agkistrodon blomhoffii bre-vicaudus (i.e. Agkistrodon halys pallas) covalently modified with p-bromo-phenacylbromide wereobtained by the method of hanging drop vapor diffusion. Crystallization droplet was composedof 0.06mol’L-1 Na(CH3)2AsO2 (pH=6.5), 24.8% (v/v) 1,4-butanediol, and 4.5mg.mL-1 protein.The crystal data are ot a=b=82.82A., c=32.85A, space group P61. 8945 unique reflections with1.93A resolution were ineasured on a Siemens area detector X-ray diffractometor, of which 8069reflections haring F0 >2σ(F). The experimental results show that the crystals are suitable to astructure analysis of high resolution.展开更多
Phospholipase A<sub>2</sub> catalyzes specially the hydrolysis of the ester bond at the C<sub>2</sub> position of3-sn-phosphoglycerides. Besides the enzymatic activity, the venom phospholipase ...Phospholipase A<sub>2</sub> catalyzes specially the hydrolysis of the ester bond at the C<sub>2</sub> position of3-sn-phosphoglycerides. Besides the enzymatic activity, the venom phospholipase A<sub>2</sub> from varioussources displays complicated pharmacological activity and toxicity. The phospholipaseA<sub>2</sub> neurotoxin is a noteworthy group in all phospholipase A<sub>2</sub> species. It has been展开更多
D-glyceraldehyde-3-phosphate dehydrogenase (holo-GAPDH) from Palinurus versicolor was crystallized in a novel crystal form by the method of sitting-drop vapor diffusion. The crystals have space group P4212, cell param...D-glyceraldehyde-3-phosphate dehydrogenase (holo-GAPDH) from Palinurus versicolor was crystallized in a novel crystal form by the method of sitting-drop vapor diffusion. The crystals have space group P4212, cell parameters a=15.49 nm, c=8.03 nm and two subunits per asymmetric unit. The crystal structure at 0.34 nm was determined by the molecular replacement method. The final model has crystallographic Rfree and R factors of 0.274 and 0.262, and r.m.s. deviations of 0.002 nm for bond lengths and 2.33?for bond angles. The two subunits in asymmetric unit are similar to each other not only in the three-dimensional structure, but also in average temperature factors. This result demonstrates that the obvious difference in average temperature factors for the different subunits in C2 crystal form reported previously may be attributed to the different crystallographic environments of the subunits. This further supports that holo-GAPDH has a good 222 molecular symmetry.展开更多
Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzym...Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzymes were calculated respectively. The statistical results showed that the critical residues at the active site of most of the enzymes had lower B factors than did the whole molecules, indicating that in the crystalline state the critical residues at the active site of the natural enzymes possess more stable conformation than do the whole molecules. The flexibility of the active site during the unfolding by denaturing was also discussed.展开更多
The basic phospholipase A2 from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. The accurate rotation and translation parameters of the molecules in orthorhombic crystal form I wer...The basic phospholipase A2 from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. The accurate rotation and translation parameters of the molecules in orthorhombic crystal form I were successfully obtained using the fitting refinement technique. The structure was refined in the resolution range of 0. 6-0.25 nm using least square refinement with non-crystallographic two fold symmetry restraint, and resulted in the final R factor of 20.1 % , and the rms deviations from ideal stereochemistry were 0. 001 3 nm for bond lengths and 1. 32° for bond angles. The overall architecture of the present structure was similar to that of the determined structure of the orthorhombic crystal form Ⅱ, with a few differences in the regions of the β-wing and Ca2 +-binding loop. The dimers formed by the two molecules in the asymmetric unit in both crystal forms were also similar. However, one of the monomers showed an orientational difference of 5.5° along the dimer interface in the two展开更多
文摘The Crystals of acidic phospholipase A2 from the venom of Agkistrodon blomhoffii bre-vicaudus (i.e. Agkistrodon halys pallas) covalently modified with p-bromo-phenacylbromide wereobtained by the method of hanging drop vapor diffusion. Crystallization droplet was composedof 0.06mol’L-1 Na(CH3)2AsO2 (pH=6.5), 24.8% (v/v) 1,4-butanediol, and 4.5mg.mL-1 protein.The crystal data are ot a=b=82.82A., c=32.85A, space group P61. 8945 unique reflections with1.93A resolution were ineasured on a Siemens area detector X-ray diffractometor, of which 8069reflections haring F0 >2σ(F). The experimental results show that the crystals are suitable to astructure analysis of high resolution.
基金Project supported by the Chinese Academy of Science.
文摘Phospholipase A<sub>2</sub> catalyzes specially the hydrolysis of the ester bond at the C<sub>2</sub> position of3-sn-phosphoglycerides. Besides the enzymatic activity, the venom phospholipase A<sub>2</sub> from varioussources displays complicated pharmacological activity and toxicity. The phospholipaseA<sub>2</sub> neurotoxin is a noteworthy group in all phospholipase A<sub>2</sub> species. It has been
文摘D-glyceraldehyde-3-phosphate dehydrogenase (holo-GAPDH) from Palinurus versicolor was crystallized in a novel crystal form by the method of sitting-drop vapor diffusion. The crystals have space group P4212, cell parameters a=15.49 nm, c=8.03 nm and two subunits per asymmetric unit. The crystal structure at 0.34 nm was determined by the molecular replacement method. The final model has crystallographic Rfree and R factors of 0.274 and 0.262, and r.m.s. deviations of 0.002 nm for bond lengths and 2.33?for bond angles. The two subunits in asymmetric unit are similar to each other not only in the three-dimensional structure, but also in average temperature factors. This result demonstrates that the obvious difference in average temperature factors for the different subunits in C2 crystal form reported previously may be attributed to the different crystallographic environments of the subunits. This further supports that holo-GAPDH has a good 222 molecular symmetry.
文摘Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzymes were calculated respectively. The statistical results showed that the critical residues at the active site of most of the enzymes had lower B factors than did the whole molecules, indicating that in the crystalline state the critical residues at the active site of the natural enzymes possess more stable conformation than do the whole molecules. The flexibility of the active site during the unfolding by denaturing was also discussed.
基金Project supported by the Chinese Academy of Sciences.
文摘The basic phospholipase A2 from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. The accurate rotation and translation parameters of the molecules in orthorhombic crystal form I were successfully obtained using the fitting refinement technique. The structure was refined in the resolution range of 0. 6-0.25 nm using least square refinement with non-crystallographic two fold symmetry restraint, and resulted in the final R factor of 20.1 % , and the rms deviations from ideal stereochemistry were 0. 001 3 nm for bond lengths and 1. 32° for bond angles. The overall architecture of the present structure was similar to that of the determined structure of the orthorhombic crystal form Ⅱ, with a few differences in the regions of the β-wing and Ca2 +-binding loop. The dimers formed by the two molecules in the asymmetric unit in both crystal forms were also similar. However, one of the monomers showed an orientational difference of 5.5° along the dimer interface in the two
