Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound details
SEE REMARK 999
Sequence details
BOTH THE HIV-1 PROTEASE COVALENT DIMER [L-ALA51,D-ALA51'] (CHAINS A AND B) AND JG-365 INHIBITOR ...BOTH THE HIV-1 PROTEASE COVALENT DIMER [L-ALA51,D-ALA51'] (CHAINS A AND B) AND JG-365 INHIBITOR (CHAINS C AND D) WERE CHEMICALLY SYNTHESIZED WITH NON-NATURAL AMINO ACIDS INTRODUCED AT SEVERAL POSITIONS. THE HIV-1 PROTEASE DIMER HAS TWO COVALENTLY LINKED MONOMER PARTS, RESIDUES 1-99 AND RESIDUES 105-203, BOTH REPRESENTING ANALOGUE OF HIV-1 PROTEASE CORRESPONDING TO THE RESIDUES 491-589 OF UNP ENTRY P03369. THE REGION 1-99 OF THE FIRST HALF AND 105-203 OF THE SECOND HALF SHARE THE SAME SEQUENCE EXCEPT FOR THE 51ST RESIDUE, WHICH IS L-ALA(ALA51) IN REGION 1-99 AND D-ALA (DAL155) IN REGION 105-203. THERE IS A SHORT LINKER REGION (RESIDUES 100-104). THE TWO REGIONS (HALVES) ARE RELATED BY INTRA-MOLECULAR PSEUDO-2-FOLD SYMMETRY, I.E. REGIONS 1-99 AND 105-203 HAVE SIMILAR STRUCTURES BUT DO NOT SUPERIMPOSE COMPLETELY. MOREOVER, THERE IS A DISORDER WITH RESPECT TO THE NON-CRYSTALLOGRAPHIC PSEUDO-2-FOLD SYMMETRY AXIS OF THE COVELENT DIMER HIV-1 PROTEASE. SUCH CONCLUSION IS BASED ON THE SPLIT OF THE DENSITY AT THE BETA-TURN REGIONS FOR RESIDUES 49-52 AND 153-156, ALTHOUGH THE IS NO DENSITY SPLIT BETWEEN TWO CONFORMERS FOR MOST OF THE ATOMS. TO ACCOUNT FOR SUCH DISORDER, CHAINS A AND B, EACH REPRESENTING THE SAME 203-AMINO ACID RESIDUE COVALENT DIMER HIV-1 PROTEASE WERE INTRODUCED IN THE STRUCTURE SOLUTION. SO WERE CHAINS C AND D FOR THE PEPTIDOMIMETIC JG-365 INHIBITOR, WHERE CHAIN C OF INHIBITOR CORRESPONDS TO THE MODEL A OF THE COVELENT DIMER HIV-1 PROTEASE AND CHAIN D CORRESPONDS TO MODEL B. THESE TWO MODELS, OR TWO CONFORMATIONS OF ONE POLYMER CHAIN ARE RELATED TO EACH OTHER BY PSEUDO-2-FOLD SYMMETRY. THE OCCUPANCIES WERE DETERMINED TO BE 0.65 FOR CHAINS A AND C AND 0.35 FOR CHAINS B AND D, RESPECTIVELY.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2 Å3/Da / Density % sol: 38.57 %
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2007 Details: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Radiation
Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.486 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SEE REMARK 999 FOR THE SPECIAL STRUCTURAL SOLUTION
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23682
883
5.1 %
RANDOM
Rwork
0.18778
-
-
-
obs
0.19016
16579
99.9 %
-
all
-
16579
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 20.294 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.65 Å2
0 Å2
0 Å2
2-
-
0.23 Å2
0 Å2
3-
-
-
0.42 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3212
0
0
96
3308
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1774
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.673
1.982
2403
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.43
5
228
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
43.139
25.082
61
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.533
15
303
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.514
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.123
0.2
279
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1259
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
745
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.32
0.2
1163
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.2
106
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.044
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.175
0.2
52
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.195
0.2
9
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.057
1.5
1171
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.557
2
1839
X-RAY DIFFRACTION
r_scbond_it
2.569
3
685
X-RAY DIFFRACTION
r_scangle_it
3.931
4.5
564
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.801→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.234
59
-
Rwork
0.181
1206
-
obs
-
-
100 %
+
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