Author states that inhibitor IMPI alpha maintains its 3D structure (represented by chains C,I and D,J) after being cleaved between residues 56-57. The biological assemnbly is a dimeric complex between a proteinase moiety (chains A or B) and an inhibitor moiety (chains C,I or D,J) indicated as trimeric in remark 350.
-
Components
-
Protein , 1 types, 2 molecules AB
#1: Protein
Thermolysin / Thermostable neutral proteinase
Mass: 34360.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.423 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1931
793
1.3 %
RANDOM
Rwork
0.15863
-
-
-
all
0.15911
59746
-
-
obs
0.15911
58951
99.51 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 28.338 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.23 Å2
0 Å2
0.23 Å2
2-
-
-1.06 Å2
0 Å2
3-
-
-
-1.17 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5842
0
28
610
6480
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.021
6031
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3860
X-RAY DIFFRACTION
r_angle_refined_deg
1.314
1.931
8167
X-RAY DIFFRACTION
r_angle_other_deg
0.908
3
9388
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.036
5
752
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.049
24.698
298
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.527
15
888
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.626
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
866
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
6910
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1256
X-RAY DIFFRACTION
r_mcbond_it
0.639
1.5
3752
X-RAY DIFFRACTION
r_mcbond_other
0.183
1.5
1576
X-RAY DIFFRACTION
r_mcangle_it
1.065
2
5979
X-RAY DIFFRACTION
r_scbond_it
1.761
3
2279
X-RAY DIFFRACTION
r_scangle_it
2.725
4.5
2188
LS refinement shell
Resolution: 1.803→1.85 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
49
-
Rwork
0.207
4150
-
obs
-
-
94.81 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.0107
0.2785
0.4391
0.8266
-0.3214
1.4555
-0.0516
0.0185
-0.0426
-0.0045
-0.019
-0.1282
-0.036
-0.0319
0.0705
0.0361
-0.0204
0.0198
0.074
-0.0211
0.1475
22.202
21.505
38.712
2
0.9429
0.0458
-0.7159
0.2895
0.2834
1.6784
0.0125
-0.0562
0.0294
0.0419
-0.0344
0.0912
0.052
0.0184
0.0219
0.1401
-0.0586
-0.0107
0.1524
0.0246
0.1458
1.877
17.886
84.736
3
2.7191
2.0447
0.839
12.837
1.4474
1.1042
0.1715
0.185
-0.0442
-1.145
-0.2347
0.8176
-0.0911
-0.1043
0.0631
0.1653
0.0618
-0.0846
0.1916
-0.0088
0.2267
6.06
0.329
33.915
4
2.7198
3.413
-1.881
16.7045
-2.2085
1.6664
0.1606
-0.0391
0.0984
-1.3812
-0.2265
-0.6367
0.027
-0.0149
0.0659
0.3128
0.0263
0.1069
0.2149
0.0106
0.1828
16.673
39.589
80.018
5
0.2026
0.095
-0.1682
0.1736
-0.0207
0.65
0.0014
-0.0144
-0.0228
0.0255
-0.014
-0.0182
0.0082
-0.0193
0.0125
0.1991
-0.0116
-0.0145
0.2315
0.0067
0.2831
13.19
19.091
56.367
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 316
2
X-RAY DIFFRACTION
1
A
999
3
X-RAY DIFFRACTION
1
A
998
4
X-RAY DIFFRACTION
1
A
997
5
X-RAY DIFFRACTION
1
A
996
6
X-RAY DIFFRACTION
1
A
995
7
X-RAY DIFFRACTION
2
B
1 - 316
8
X-RAY DIFFRACTION
2
B
999
9
X-RAY DIFFRACTION
2
B
998
10
X-RAY DIFFRACTION
2
B
997
11
X-RAY DIFFRACTION
2
B
996
12
X-RAY DIFFRACTION
2
B
995
13
X-RAY DIFFRACTION
3
I
57 - 86
14
X-RAY DIFFRACTION
3
C
22 - 56
15
X-RAY DIFFRACTION
4
J
57 - 85
16
X-RAY DIFFRACTION
4
D
23 - 56
17
X-RAY DIFFRACTION
5
C
595 - 1112
18
X-RAY DIFFRACTION
5
D
762 - 1101
19
X-RAY DIFFRACTION
5
I
501
20
X-RAY DIFFRACTION
5
J
853 - 1108
+
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