- PDB-3nje: Structure of the Minor Pseudopilin XcpW from the Pseudomonas aeru... -
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Basic information
Entry
Database: PDB / ID: 3nje
Title
Structure of the Minor Pseudopilin XcpW from the Pseudomonas aeruginosa Type II Secretion System
Components
General secretion pathway protein J
Keywords
PROTEIN TRANSPORT / Type II secretion / Pseudopilin / minor pilin / pilin fold / secretion / XcpU / XcpV / XcpX
Function / homology
Function and homology information
protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane Similarity search - Function
Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like Similarity search - Domain/homology
Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.111 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2304
1545
5 %
RANDOM
Rwork
0.1944
-
-
-
obs
0.19631
29187
99.64 %
-
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: 19.937 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.06 Å2
0 Å2
-0.07 Å2
2-
-
1.79 Å2
0 Å2
3-
-
-
-0.77 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.136 Å
0.147 Å
Refinement step
Cycle: LAST / Resolution: 1.85→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2668
0
0
193
2861
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.021
2729
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.24
1.946
3688
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.301
5
319
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.574
22.658
158
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.556
15
492
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.648
15
42
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
381
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2132
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
0.728
1.5
1590
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.367
2
2552
X-RAY DIFFRACTION
r_scbond_it
1.926
3
1139
X-RAY DIFFRACTION
r_scangle_it
3.21
4.5
1135
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.254
89
-
Rwork
0.224
2161
-
obs
-
-
98.38 %
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
13.5784
-9.5622
-4.9676
10.978
2.6963
3.0545
-0.0691
-0.1906
-0.6675
0.1119
-0.1208
0.2689
0.3992
0.043
0.1899
0.2161
-0.0091
-0.0277
0.0292
0.0236
0.0956
34.0584
1.6028
26.5814
2
8.6766
-3.1325
0.0535
3.6189
0.4719
2.8816
-0.0196
0.1564
-0.3643
0.1133
-0.1847
0.3562
0.1752
-0.2319
0.2044
0.0372
-0.0286
0.0299
0.033
-0.028
0.068
16.2934
14.8159
29.4628
3
0.2152
-0.6661
-0.7838
2.1927
2.3561
3.3308
0.0141
-0.0099
0.0481
0.1152
-0.0438
-0.0904
-0.1709
0.1318
0.0298
0.1969
-0.0372
-0.0092
0.1317
-0.054
0.1804
18.7688
29.9082
37.9579
4
8.4548
0.4929
-2.4951
4.0872
-0.5582
6.5016
-0.2021
-0.4885
-0.065
0.0149
-0.0203
-0.0829
0.0126
0.3092
0.2225
0.0138
0.016
-0.002
0.0523
-0.0129
0.0376
22.621
20.9979
32.6604
5
2.6696
-0.5198
-0.0103
1.8199
0.4591
2.312
-0.0916
-0.2493
0.1625
0.0968
0.0794
0.0506
-0.1364
0.0036
0.0122
0.0218
0.0023
0.0066
0.0477
-0.0188
0.053
24.6453
20.9675
31.6684
6
3.8998
-0.8409
-0.2295
1.1828
0.4775
1.9572
0.0174
0.2414
0.0769
-0.0281
-0.0404
0.0695
-0.0762
-0.1377
0.023
0.0101
-0.0006
-0.001
0.0378
-0.0103
0.0425
20.1534
20.1203
23.3226
7
16.3802
-3.3338
-12.7405
19.3544
6.1178
20.7927
-0.3673
1.2752
-1.2013
-0.9734
-0.3875
-1.5081
1.0933
1.1821
0.7548
0.3338
0.1234
0.0722
0.6036
-0.0166
0.3625
34.4263
37.747
37.2192
8
2.8196
-0.0657
-0.3927
1.9331
0.5294
3.2021
-0.0074
-0.1896
-0.1551
0.2026
-0.0032
0.0373
0.2308
-0.2126
0.0107
0.0617
-0.0476
-0.0102
0.069
0.0235
0.0293
17.1352
42.8439
56.3234
9
1.2879
-0.8633
-0.2625
1.1092
0.7567
1.6236
0.0367
-0.2104
-0.3144
0.1547
-0.0766
0.0513
0.3316
-0.0694
0.0399
0.1636
-0.0714
-0.0172
0.1682
0.1013
0.1906
20.6449
37.9174
56.0567
10
4.3507
0.9831
-1.1176
1.5072
-0.2211
1.8537
-0.0783
0.035
-0.3139
-0.0668
0.0717
-0.2548
0.3124
0.1861
0.0066
0.0673
0.0138
-0.0173
0.1004
0.0217
0.0848
33.6634
43.0303
48.8311
11
2.6869
0.7697
-1.1899
1.4435
-1.2024
5.6826
0.1209
-0.0607
0.4166
0.1761
0.0145
0.1377
-0.5289
-0.4754
-0.1354
0.0558
0.0313
0.0202
0.0823
-0.0296
0.0725
16.5721
56.9388
58.0831
12
7.4868
0.0035
-1.9765
0.5265
-0.3084
1.8642
0.0069
0.2634
0.0556
-0.1144
-0.02
0.0024
0.118
-0.0706
0.0131
0.0281
-0.0029
0.001
0.0803
0.0166
0.0192
23.1232
49.9901
45.8013
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
41 - 53
2
X-RAY DIFFRACTION
2
A
54 - 67
3
X-RAY DIFFRACTION
3
A
68 - 83
4
X-RAY DIFFRACTION
4
A
84 - 109
5
X-RAY DIFFRACTION
5
A
110 - 166
6
X-RAY DIFFRACTION
6
A
167 - 206
7
X-RAY DIFFRACTION
7
B
43 - 50
8
X-RAY DIFFRACTION
8
B
51 - 80
9
X-RAY DIFFRACTION
9
B
81 - 138
10
X-RAY DIFFRACTION
10
B
139 - 149
11
X-RAY DIFFRACTION
11
B
150 - 179
12
X-RAY DIFFRACTION
12
B
180 - 206
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