A: Signal peptide peptidase sppA B: Signal peptide peptidase sppA C: Signal peptide peptidase sppA D: Signal peptide peptidase sppA E: Signal peptide peptidase sppA F: Signal peptide peptidase sppA G: Signal peptide peptidase sppA H: Signal peptide peptidase sppA
Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence details
AUTHOR STATES THE EXPRESSED PROTEIN(36000DA) IS COMPOSED OF AN N-TERMINAL HISTINE AFFINITY TAG WITH ...AUTHOR STATES THE EXPRESSED PROTEIN(36000DA) IS COMPOSED OF AN N-TERMINAL HISTINE AFFINITY TAG WITH LINKER REGION (MGSSHHHHHHSSGLVPAGSH-) PLUS RESIDUES 26-335 OF THE SPPA. THE PURIFIED PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BEFORE CRYSTALLIZATION WHICH RESULTED IN A FINAL SIZE PROTEIN ABOUT 28000DA. SEQRES RECORD REPRESENTS SEQUENCE EXTRACTED FROM COORDINATES (RESIDUES FROM 56 TO 295).
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.67 Å3/Da / Density % sol: 54.04 %
Crystal grow
Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100mM Tris pH 8.5 23% Tert-butanol 5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution: 2.37→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.691 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24052
4806
5 %
RANDOM
Rwork
0.20571
-
-
-
obs
0.20748
91450
98.16 %
-
all
-
95998
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 48.998 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.34 Å2
0 Å2
0 Å2
2-
-
1.1 Å2
0 Å2
3-
-
-
-0.76 Å2
Refinement step
Cycle: LAST / Resolution: 2.37→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13685
0
0
257
13942
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
13855
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.135
1.977
18582
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.31
5
1787
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.545
25.395
532
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.322
15
2658
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.573
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.074
0.2
2110
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
9989
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
0.443
1.5
8884
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.888
2
14224
X-RAY DIFFRACTION
r_scbond_it
1.648
3
4971
X-RAY DIFFRACTION
r_scangle_it
2.736
4.5
4357
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.37→2.428 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.293
263
-
Rwork
0.238
5440
-
obs
-
-
79.43 %
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
3.5257
1.6764
0.9739
16.6362
3.688
5.5837
-0.2303
0.1847
-0.1157
-0.9839
0.3173
-0.3592
-0.1812
0.124
-0.0871
0.0687
-0.013
0.0472
0.2037
0.0018
0.1324
-46.8791
-39.213
19.9048
2
2.3796
1.4354
0.3698
1.3174
-0.2147
0.9875
-0.0191
-0.0125
-0.1952
-0.1196
-0.0012
-0.2719
-0.0521
0.0758
0.0204
0.0922
-0.0106
0.0431
0.0992
-0.0382
0.1211
-45.8092
-40.6488
25.3521
3
2.4807
1.767
0.724
3.3633
0.1325
3.1806
0.0316
-0.0704
0.0046
0.1564
-0.034
-0.0765
-0.0275
-0.0337
0.0024
0.0317
0.0107
0.0126
0.1044
-0.0426
0.0424
-56.6728
-40.5466
27.0193
4
0.1993
0.0706
0.8991
0.0595
0.2192
7.4897
0.0373
0.1074
0.0327
-0.0429
0.0464
0.1098
-0.2445
-0.4225
-0.0837
0.3091
0.0817
-0.0734
0.374
-0.0441
0.3465
-55.7888
-76.5766
14.7323
5
1.4773
0.1448
0.042
2.7715
-0.283
1.2992
0.0146
-0.1112
0.1346
0.2196
-0.0383
0.0859
-0.136
-0.1302
0.0237
0.0583
0.0239
0.0029
0.229
-0.0511
0.0346
-61.6626
-42.0232
27.7686
6
2.8717
4.6609
-0.5063
12.8468
-0.2979
4.7381
-0.0441
-0.0311
0.2663
0.6377
-0.0794
-0.7288
-0.5659
0.8354
0.1235
0.2904
-0.046
-0.0795
0.4889
0.0768
0.459
-52.8861
-22.5957
3.9386
7
2.355
0.7408
-0.195
3.0061
-1.7558
4.6521
-0.0232
-0.2125
0.2452
0.2454
-0.1485
-0.2575
-0.5547
0.3178
0.1718
0.1494
0.0352
-0.0277
0.206
-0.0176
0.1518
-64.4528
-24.9927
0.9918
8
0.2822
-0.724
-1.3762
2.1084
3.8983
7.2757
-0.0359
0.0604
0.033
-0.1089
0.0677
0.0167
-0.0273
0.0997
-0.0318
0.5086
0.0435
-0.0943
0.398
-0.0008
0.2831
-67.8926
-60.6348
10.8394
9
1.2967
0.5005
-0.0147
2.6612
-1.7621
3.5794
-0.0044
-0.0007
0.2365
0.0053
0.078
0.1545
-0.4555
-0.2928
-0.0735
0.1466
0.0916
-0.0077
0.2435
-0.0642
0.1535
-73.7413
-28.2493
-0.5306
10
9.9422
-1.1648
-0.8632
8.2722
1.1343
3.9591
-0.3305
-0.1032
1.0556
0.3162
0.158
-0.9805
-0.6528
-0.0794
0.1725
0.842
-0.1157
-0.0692
0.5632
0.1115
0.6762
-55.4717
-9.2315
-3.771
11
4.2213
1.6016
-0.6501
3.2001
-0.1385
4.9927
0.0133
-0.2613
0.0662
0.4283
-0.0606
-0.341
-0.0784
0.2996
0.0473
0.1038
0.047
-0.0523
0.2947
0.0271
0.1994
-47.9472
-24.3396
-24.7772
12
3.7269
0.766
-0.5835
2.5947
0.2089
3.1928
-0.0191
-0.2877
0.0491
0.0691
-0.1795
-0.0478
0.0135
0.148
0.1986
0.0702
0.062
-0.0089
0.1099
0.0266
0.0581
-58.4912
-28.3112
-29.1661
13
1.974
-5.0561
-0.229
13.0909
0.4422
0.1871
0.0166
0.0367
-0.0482
-0.2775
-0.0351
0.0676
0.2853
-0.0411
0.0185
0.5293
-0.0218
-0.038
0.3493
-0.0236
0.235
-74.0797
-50.3608
-5.9266
14
3.3776
1.1658
-0.9324
1.7143
-0.4734
2.2666
-0.0772
0.2524
0.0475
-0.1971
0.0001
-0.0385
-0.0533
-0.1572
0.0771
0.1315
0.0897
-0.0224
0.0954
0.003
0.0894
-64.8217
-30.6456
-35.2493
15
4.5295
-0.73
7.3452
0.1338
-1.2132
12.0731
-0.2382
-0.1864
0.1491
0.0879
0.1291
-0.0095
-0.6434
-0.358
0.1091
0.4201
0.0413
0.0524
0.5669
0.103
0.4148
-41.6882
-18.8333
-32.9987
16
5.7546
1.8386
-2.7016
4.1067
-2.032
2.9311
0.2539
-0.5804
0.65
0.3921
-0.2828
-0.5869
-0.8731
0.5748
0.0289
0.5677
-0.0301
-0.0002
0.6131
-0.1249
0.7119
-33.3276
-39.914
-40.5785
17
3.3459
0.1623
-0.8378
1.8011
-0.1311
2.8422
0.2959
-0.2716
1.1204
-0.0349
-0.0554
-0.3866
-0.8045
0.3339
-0.2404
0.418
0.0386
0.1396
0.2701
-0.0114
0.5771
-38.1984
-40.4171
-46.6594
18
4.1887
-0.0516
1.6934
3.8876
-0.2143
1.2278
0.2171
-0.2873
0.4246
-0.3529
-0.1388
-0.2536
-0.0614
0.2033
-0.0783
0.2738
0.0121
0.1908
0.3005
-0.0936
0.2785
-40.1513
-50.6198
-49.0847
19
0.1704
-1.066
0.6463
8.4072
-5.3486
3.4614
-0.035
-0.0362
-0.1127
-0.2783
-0.003
0.0528
0.3405
0.0209
0.038
0.4906
0.0621
0.1125
0.2917
0.0223
0.3785
-68.8012
-52.545
-26.1443
20
4.3121
-0.8163
-1.5183
2.1873
0.4359
2.5108
0.2223
0.3122
0.3601
-0.3391
-0.162
-0.4972
-0.2831
0.2101
-0.0603
0.3285
0.0831
0.0525
0.201
0.0778
0.2259
-41.152
-50.9274
-53.7795
21
7.5368
3.6872
0.2866
3.6219
0.345
2.6446
0.0875
-0.1674
0.8753
0.0764
-0.2097
-0.3573
-0.5464
0.445
0.1222
0.4112
-0.0323
-0.0779
0.3444
0.0597
0.6175
-16.8838
-60.7137
-37.5533
22
2.9933
0.1113
1.5369
2.8637
-0.3108
2.102
-0.0764
0.0685
0.7006
-0.0896
-0.2116
-0.6031
-0.198
0.4102
0.288
0.1634
0.055
0.0676
0.1911
0.0591
0.3392
-19.7573
-70.7283
-42.118
23
0.4156
0.3551
-1.4514
0.5469
-1.6676
6.0459
-0.0312
-0.0973
-0.1125
0.0364
0.1445
0.1674
0.3244
0.0139
-0.1132
0.4565
0.0984
0.0703
0.3524
0.1171
0.4678
-56.0681
-66.0048
-37.1101
24
3.4719
-0.424
0.7388
2.6957
-0.7474
2.4255
0.025
0.3084
-0.0416
-0.3502
-0.2071
-0.4108
0.1184
0.383
0.1821
0.2143
0.0386
0.0911
0.1189
0.044
0.0829
-24.1324
-79.8257
-44.8326
25
48.4934
4.9058
-3.991
0.5953
-0.3716
0.3565
0.4994
-1.3542
1.3887
-0.1001
-0.2704
-0.1853
-0.1793
0.248
-0.229
0.9314
-0.5579
0.113
1.6126
0.5858
1.3693
-2.484
-68.6893
-40.0439
26
5.7157
0.8194
0.7738
2.8715
-0.952
4.305
-0.0414
0.2047
0.9231
-0.1143
-0.1013
-0.1589
-0.503
0.1204
0.1427
0.3028
-0.016
-0.0223
0.0797
-0.0234
0.2842
-8.0568
-77.2582
-14.3519
27
3.6282
1.1738
1.3491
2.1198
0.0997
3.5177
-0.1123
0.1022
0.3756
-0.1219
-0.0445
-0.051
-0.1826
-0.023
0.1568
0.0986
0.0412
0.0068
0.0257
0.019
0.0679
-13.7445
-87.8627
-16.2924
28
7.5908
-2.3549
-5.9954
0.7502
1.822
4.8971
-0.1217
-0.2794
-0.1722
0.0728
0.1283
0.1332
0.0797
-0.0169
-0.0067
0.3074
0.0367
0.0793
0.3914
0.136
0.3535
-44.6632
-81.9409
-32.2517
29
3.8266
0.2232
2.5786
1.0266
-0.2393
3.0607
0.1217
0.0048
-0.1238
-0.063
-0.0341
-0.0552
0.2086
0.1113
-0.0876
0.1026
0.0328
0.0453
0.0213
0.0038
0.0439
-15.5903
-96.2879
-15.3448
30
7.4489
-1.7056
0.0717
9.5477
2.0086
3.6316
0.0289
-0.0993
1.1288
0.2503
-0.0715
-0.7193
-0.2721
0.2905
0.0426
0.2399
-0.0519
-0.0061
0.3215
0.009
0.3105
3.5234
-82.6803
-6.6883
31
7.1935
1.3606
1.8961
3.5615
1.5462
5.6213
-0.0421
0.2301
0.5695
-0.0407
-0.0358
-0.4799
-0.407
1.0131
0.0779
0.3567
-0.1662
0.01
0.4046
-0.0145
0.326
-11.4444
-77.9893
12.8572
32
2.9856
0.3619
-0.248
2.563
0.5742
4.296
0.0647
-0.0205
0.0068
0.0311
0.0144
-0.3012
-0.2508
0.6713
-0.0791
0.0919
-0.0472
-0.0284
0.1624
-0.0234
0.0569
-19.1382
-87.0326
14.456
33
7.3062
-5.7241
-2.4135
4.4926
1.8853
0.8305
0.1581
0.2118
-0.0211
-0.0939
-0.1474
0.0479
-0.0747
-0.1826
-0.0108
0.2334
0.0379
0.0233
0.3979
0.0781
0.1757
-40.4719
-90.4319
-15.3992
34
2.0861
-0.0088
0.4469
1.3997
0.1721
3.7396
0.0638
-0.1986
-0.1019
0.174
0.0532
-0.2409
0.33
0.393
-0.117
0.1039
0.0202
-0.0174
0.1248
0.0309
0.0946
-25.7701
-94.1116
15.662
35
7.3196
-0.3103
-0.2427
9.3599
-5.5523
6.6413
0.1728
-0.4521
0.0423
0.4956
-0.3748
-0.5706
-0.3295
0.9662
0.202
0.5406
-0.1687
-0.1823
0.8192
-0.1372
0.4401
-7.0455
-78.1576
27.4816
36
4.4802
1.8949
4.3826
5.2284
2.6823
6.2015
-0.1526
0.3229
0.2695
-0.2127
0.1808
-0.6212
-0.4786
0.4566
-0.0282
0.3289
-0.076
-0.03
0.2309
0.0112
0.3337
-26.9793
-61.1488
26.6853
37
2.4205
0.192
0.1831
3.6876
0.5062
1.8211
-0.2866
-0.0895
0.1788
0.1034
0.2005
-0.3574
-0.1703
0.1167
0.0861
0.2248
0.0007
-0.0641
0.0972
-0.048
0.0716
-35.4324
-65.7775
32.7242
38
3.0371
-0.4587
0.7258
4.7129
0.1075
11.01
0.1814
-0.0493
0.0362
0.0858
-0.1725
-0.1337
-0.1228
0.107
-0.0089
0.1599
-0.0074
0.0378
0.308
0.0384
0.1748
-48.2478
-85.1992
0.7347
39
0.266
-0.5046
-0.0838
1.9829
1.4649
1.7728
-0.0106
-0.0653
-0.0135
0.0472
0.0928
0.0052
-0.0279
-0.0351
-0.0822
0.1279
-0.0488
0.0157
0.1037
0.0312
0.0618
-41.3463
-86.8525
19.9146
40
3.6048
0.9535
0.7395
3.7727
0.6703
1.5424
-0.1947
-0.4165
0.4526
0.3397
0.03
-0.2238
-0.2378
-0.009
0.1647
0.3321
0.0925
-0.1014
0.2393
-0.0715
0.1467
-41.5258
-61.6821
38.5539
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
56 - 85
2
X-RAY DIFFRACTION
2
A
86 - 122
3
X-RAY DIFFRACTION
3
A
123 - 174
4
X-RAY DIFFRACTION
4
A
175 - 210
5
X-RAY DIFFRACTION
5
A
211 - 291
6
X-RAY DIFFRACTION
6
B
57 - 103
7
X-RAY DIFFRACTION
7
B
104 - 173
8
X-RAY DIFFRACTION
8
B
174 - 210
9
X-RAY DIFFRACTION
9
B
211 - 277
10
X-RAY DIFFRACTION
10
B
278 - 290
11
X-RAY DIFFRACTION
11
C
57 - 109
12
X-RAY DIFFRACTION
12
C
110 - 175
13
X-RAY DIFFRACTION
13
C
176 - 215
14
X-RAY DIFFRACTION
14
C
216 - 277
15
X-RAY DIFFRACTION
15
C
278 - 295
16
X-RAY DIFFRACTION
16
D
57 - 99
17
X-RAY DIFFRACTION
17
D
100 - 132
18
X-RAY DIFFRACTION
18
D
133 - 175
19
X-RAY DIFFRACTION
19
D
176 - 215
20
X-RAY DIFFRACTION
20
D
216 - 290
21
X-RAY DIFFRACTION
21
E
57 - 99
22
X-RAY DIFFRACTION
22
E
100 - 173
23
X-RAY DIFFRACTION
23
E
174 - 215
24
X-RAY DIFFRACTION
24
E
216 - 277
25
X-RAY DIFFRACTION
25
E
278 - 290
26
X-RAY DIFFRACTION
26
F
57 - 109
27
X-RAY DIFFRACTION
27
F
110 - 175
28
X-RAY DIFFRACTION
28
F
176 - 215
29
X-RAY DIFFRACTION
29
F
216 - 277
30
X-RAY DIFFRACTION
30
F
278 - 291
31
X-RAY DIFFRACTION
31
G
57 - 108
32
X-RAY DIFFRACTION
32
G
109 - 174
33
X-RAY DIFFRACTION
33
G
175 - 209
34
X-RAY DIFFRACTION
34
G
210 - 276
35
X-RAY DIFFRACTION
35
G
277 - 291
36
X-RAY DIFFRACTION
36
H
56 - 99
37
X-RAY DIFFRACTION
37
H
100 - 173
38
X-RAY DIFFRACTION
38
H
174 - 191
39
X-RAY DIFFRACTION
39
H
192 - 236
40
X-RAY DIFFRACTION
40
H
237 - 291
+
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