- PDB-3pe9: Structures of Clostridium thermocellum CbhA fibronectin(III)-like... -
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Basic information
Entry
Database: PDB / ID: 3pe9
Title
Structures of Clostridium thermocellum CbhA fibronectin(III)-like modules
Components
Fibronectin(III)-like module
Keywords
UNKNOWN FUNCTION / CbhA / beta-sandwich / Cellulosome
Function / homology
Function and homology information
cellulose binding / cellulase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / metal ion binding Similarity search - Function
Bacterial Ig domain / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 ...Bacterial Ig domain / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology
This structure contains the second fibronectin(III)-like module from clostridium thermocellum CbhA. The biological assembly cannot be determine without the whole enzyme.
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Components
#1: Protein
Fibronectin(III)-likemodule / Glycoside hydrolase / family 9
Mass: 10938.033 Da / Num. of mol.: 4 / Fragment: unp residues 915-1003 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_0413 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DCH2
Resolution: 1.69→1.78 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.4056 / % possible all: 97.6
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Processing
Software
Name
Version
Classification
PROTEUM PLUS
datacollection
SHELX
modelbuilding
REFMAC
5.5.0109
refinement
SAINT
datareduction
PROTEUM PLUS
datascaling
SHELX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.69→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.441 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22861
1843
5 %
RANDOM
Rwork
0.18188
-
-
-
obs
0.18442
34722
87.53 %
-
all
-
34722
-
-
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: 16.602 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.4 Å2
0 Å2
-0.15 Å2
2-
-
-0.43 Å2
0 Å2
3-
-
-
0.74 Å2
Refinement step
Cycle: LAST / Resolution: 1.69→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2718
0
11
592
3321
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
3012
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1974
X-RAY DIFFRACTION
r_angle_refined_deg
1.902
1.957
4121
X-RAY DIFFRACTION
r_angle_other_deg
1.001
3
4866
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.002
5
395
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.142
25.664
143
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.14
15
512
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.906
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
458
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
3512
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
585
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
1.103
1.5
1906
X-RAY DIFFRACTION
r_mcbond_other
0.392
1.5
757
X-RAY DIFFRACTION
r_mcangle_it
1.731
2
3112
X-RAY DIFFRACTION
r_scbond_it
2.746
3
1106
X-RAY DIFFRACTION
r_scangle_it
4.031
4.5
1009
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.69→1.734 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.325
122
-
Rwork
0.282
2236
-
obs
-
-
77.34 %
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
2.8058
1.2423
1.4853
2.4735
1.0951
3.1741
-0.1267
0.2083
-0.005
-0.2556
0.0962
0.0566
-0.1704
0.0752
0.0305
0.0471
0.016
0.014
0.0508
0.0151
0.0656
18.62
56.289
30.9319
2
2.8361
-0.1882
1.2606
2.0789
0.5113
5.9328
-0.0281
0.1154
-0.0966
-0.1332
0.002
0.0954
-0.0305
-0.1283
0.0262
0.0258
0.0116
0.0297
0.0269
0.0284
0.0834
12.9614
53.2626
34.7611
3
2.0452
-0.0922
-0.6243
2.1176
-0.2123
1.6099
0.081
0.1914
-0.2378
-0.2334
0.0111
0.2435
0.1854
-0.2115
-0.0921
0.1035
0.0024
-0.0058
0.0437
0.01
0.1107
10.7013
42.9817
31.2868
4
4.2837
1.1013
-0.0404
9.2098
-1.9477
3.3792
-0.0282
-0.1568
-0.2064
0.1633
0.1506
0.7532
0.2735
-0.547
-0.1224
0.103
-0.0039
-0.0032
0.1263
-0.0007
0.0932
3.0543
48.0649
30.6226
5
2.9385
0.2525
-0.0392
1.5142
0.2965
1.7062
-0.0049
-0.0515
0.0137
0.0108
-0.0063
-0.0212
-0.0004
0.0075
0.0112
0.0479
-0.001
0.0051
0.0148
0.0043
0.0268
18.073
52.1587
40.8264
6
7.1435
4.8963
2.9775
7.0923
2.5676
4.3903
-0.0034
0.2349
-0.325
-0.2021
0.035
0.1967
0.2784
-0.2586
-0.0316
0.1035
0.0273
0.0206
0.0974
0.0041
0.0864
12.6108
41.6017
28.2704
7
1.1705
0.6214
0.7959
2.5703
1.4751
2.7179
0.0496
0.1197
-0.249
-0.0686
0.0243
0.0727
0.2044
-0.1491
-0.0739
0.0749
0.0242
0.0088
0.0899
0.0032
0.0923
19.55
46.3272
29.0075
8
2.8564
-1.5873
1.8074
4.4156
0.9064
5.1633
-0.0479
-0.2931
0.4643
0.2879
0.0459
-0.0329
-0.4212
-0.1222
0.002
0.1201
-0.0426
0.0715
0.0935
-0.0353
0.1724
25.5319
60.2979
46.1162
9
0.7383
1.5235
0.2725
4.5505
3.4679
7.396
-0.0433
0.1114
0.0959
-0.1772
-0.0014
0.302
-0.022
-0.2652
0.0446
0.096
0.0114
-0.0026
0.1138
-0.0057
0.1162
11.2764
23.2161
23.7561
10
2.231
0.7588
-0.2245
2.0814
0.2988
0.6329
-0.0382
0.0817
0.0261
-0.0894
0.0074
0.0123
-0.1246
0.0765
0.0308
0.0493
0.0033
-0.0008
0.043
0.0044
0.0645
19.0704
32.9404
37.9541
11
0.2414
0.2248
1.1268
1.3367
1.933
9.3129
-0.0465
0.071
0.0451
-0.1783
-0.0141
0.0977
-0.2514
-0.139
0.0606
0.0386
-0.0135
-0.0022
0.0804
0.0211
0.0588
11.6466
28.9894
37.4718
12
0.3827
0.0113
-0.0285
0.1983
-0.1578
0.152
-0.013
0.3061
-0.3221
-0.2893
0.0801
0.0495
0.2176
-0.1306
-0.0671
0.4286
-0.0806
-0.0431
0.3935
-0.1232
0.3926
4.1539
18.1793
19.9671
13
5.6881
0.3515
1.3235
3.3994
-0.097
2.9169
0.0717
0.1531
-0.1517
-0.242
-0.01
0.2691
0.1432
-0.233
-0.0617
0.0913
0.0057
0.0288
0.0529
0.0013
0.0679
10.4727
16.9465
33.6437
14
9.4978
-0.4293
4.6012
4.8306
-0.6766
6.3452
0.1712
0.1451
-0.2694
-0.515
-0.0243
0.5971
0.2783
-0.6146
-0.1469
0.1416
-0.0049
-0.0023
0.121
-0.0012
0.1285
4.2825
19.2037
35.3427
15
1.1842
-0.1883
-0.0043
1.4532
0.5818
2.1229
0.028
0.1368
-0.1135
-0.1136
-0.0305
0.1636
0.1194
-0.1694
0.0025
0.0472
0.0074
0.0065
0.0438
0.01
0.0543
13.8034
20.9937
34.1716
16
3.8327
0.2485
0.7631
2.1998
-0.0722
4.6739
0.0124
-0.1717
0.1252
0.2192
0.1001
-0.1396
0.0318
0.1498
-0.1124
0.044
0.0036
-0.0077
0.0506
0.0134
0.0716
24.576
31.8258
42.6315
17
2.2063
0.1069
-2.0146
8.0064
-1.3852
2.2584
-0.0943
-0.2588
-0.0964
0.3756
0.0622
-0.169
0.0188
0.0797
0.0321
0.05
-0.0007
0.0059
0.1421
0.0253
0.0846
5.0458
24.846
60.8348
18
3.0244
-0.9903
-0.9047
3.4064
-0.7102
2.8721
-0.0009
-0.0139
0.079
0.0408
-0.015
0.0086
-0.292
-0.1217
0.0159
0.049
-0.0077
-0.0052
0.0471
-0.0018
0.0801
-3.3788
33.3645
47.4705
19
2.1135
0.0496
0.5789
1.403
-0.0727
3.8937
0.0216
-0.2952
-0.272
0.2557
-0.023
-0.2374
0.275
0.25
0.0014
0.1021
-0.0175
0.0071
0.1107
-0.0055
0.1404
10.0967
23.1714
57.5905
20
4.9813
-0.132
-0.177
2.707
-0.0362
1.7633
0.0709
0.0491
-0.2124
0.0376
-0.004
-0.0899
0.1337
0.0956
-0.0669
0.0505
0.0009
0.0087
0.0174
-0.0054
0.0272
6.8119
17.6001
51.1911
21
7.669
3.2389
2.1683
5.8358
-1.6061
11.4701
0.035
0.0657
0.079
0.0099
-0.1149
-0.4738
0.0792
0.45
0.0799
0.0522
-0.0053
0.0075
0.0469
-0.0024
0.0684
14.5709
24.9617
54.4773
22
1.5496
-0.1776
0.4953
0.9961
-0.5145
1.4548
0.017
0.0051
0.0005
-0.0334
0.0089
0.046
0.0211
-0.0295
-0.0259
0.0289
-0.0026
0.0054
0.0128
-0.0146
0.0219
0.7055
22.5616
49.178
23
6.8874
-4.0214
-0.4187
5.663
0.1119
2.1669
-0.0339
-0.0202
-0.1805
0.0564
-0.0002
-0.1772
0.2158
0.2341
0.0342
0.0845
-0.0259
-0.0001
0.0738
-0.0025
0.0508
6.423
13.7018
60.4933
24
3.4162
-1.0623
1.9573
2.2622
-0.7155
6.3593
0.0301
0.1248
0.1421
-0.1275
0.0579
0.0758
-0.1153
-0.093
-0.088
0.0318
0.0004
0.0032
0.0401
-0.0194
0.0691
-7.6381
31.2546
45.2625
25
0.1134
-0.3058
0.225
5.4259
-4.5473
4.0697
-0.0188
-0.1021
-0.0163
0.2013
-0.0836
-0.2728
-0.0523
0.1986
0.1024
0.0941
0.0372
-0.0452
0.1598
-0.0193
0.1134
7.4891
49.8316
61.3011
26
2.5167
-1.0485
-0.2977
2.3514
-0.446
0.8204
-0.0395
-0.0575
0.0209
0.0648
0.0072
-0.0456
-0.0305
0.005
0.0322
0.0313
-0.0177
0.0019
0.0217
-0.0065
0.0477
1.9031
57.0913
48.085
27
6.8332
-1.4867
1.3622
3.8696
-0.6129
2.6782
0.0907
-0.0145
-0.102
0.1375
-0.0343
-0.195
0.1281
0.1921
-0.0563
0.082
-0.0058
0.0331
0.0421
-0.0003
0.0543
8.5301
43.0326
52.6698
28
1.4185
-0.2367
0.5424
2.4562
-0.381
2.224
0.0209
0.0354
-0.0405
0.0975
-0.0212
-0.1906
0.0638
0.2343
0.0002
0.043
-0.0011
0.0193
0.0465
-0.0035
0.0404
10.5379
49.1343
47.7114
29
4.6866
-2.1465
2.7765
5.3175
-3.9668
8.0381
-0.0177
-0.0522
-0.0162
0.0505
0.1076
0.1704
-0.1048
-0.2531
-0.0899
0.0466
-0.0116
-0.0012
0.0321
-0.0198
0.0615
-5.7217
49.7998
46.0067
30
7.293
-4.2308
1.8175
6.3017
-1.2927
3.0852
0.0122
-0.0632
-0.1605
0.1743
-0.0479
-0.2588
0.2353
0.3057
0.0357
0.0799
-0.0163
0.0161
0.0762
-0.0082
0.0528
9.5984
40.574
56.7755
31
1.86
-2.5535
2.1526
5.0847
-3.1192
2.6149
0.039
-0.0366
-0.1391
0.0478
0.0469
-0.0137
0.0634
0.0031
-0.0859
0.0427
-0.0119
0.0091
0.0571
0.0071
0.0684
2.2279
43.9434
57.4453
32
2.9572
1.415
0.0465
4.024
-1.0287
2.66
0.0056
0.3022
0.2702
-0.2544
0.064
0.1031
-0.1826
-0.0579
-0.0696
0.0574
0.0162
0.006
0.0648
-0.0016
0.0709
-6.6961
59.226
40.7408
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 14
2
X-RAY DIFFRACTION
2
A
15 - 27
3
X-RAY DIFFRACTION
3
A
28 - 47
4
X-RAY DIFFRACTION
4
A
48 - 52
5
X-RAY DIFFRACTION
5
A
53 - 63
6
X-RAY DIFFRACTION
6
A
64 - 73
7
X-RAY DIFFRACTION
7
A
74 - 85
8
X-RAY DIFFRACTION
8
A
86 - 90
9
X-RAY DIFFRACTION
9
B
1 - 4
10
X-RAY DIFFRACTION
10
B
5 - 17
11
X-RAY DIFFRACTION
11
B
18 - 23
12
X-RAY DIFFRACTION
12
B
24 - 26
13
X-RAY DIFFRACTION
13
B
31 - 43
14
X-RAY DIFFRACTION
14
B
44 - 49
15
X-RAY DIFFRACTION
15
B
50 - 82
16
X-RAY DIFFRACTION
16
B
83 - 90
17
X-RAY DIFFRACTION
17
C
1 - 6
18
X-RAY DIFFRACTION
18
C
7 - 17
19
X-RAY DIFFRACTION
19
C
18 - 31
20
X-RAY DIFFRACTION
20
C
32 - 48
21
X-RAY DIFFRACTION
21
C
49 - 53
22
X-RAY DIFFRACTION
22
C
54 - 71
23
X-RAY DIFFRACTION
23
C
72 - 81
24
X-RAY DIFFRACTION
24
C
82 - 90
25
X-RAY DIFFRACTION
25
D
1 - 5
26
X-RAY DIFFRACTION
26
D
6 - 24
27
X-RAY DIFFRACTION
27
D
25 - 42
28
X-RAY DIFFRACTION
28
D
43 - 58
29
X-RAY DIFFRACTION
29
D
59 - 64
30
X-RAY DIFFRACTION
30
D
65 - 73
31
X-RAY DIFFRACTION
31
D
74 - 84
32
X-RAY DIFFRACTION
32
D
85 - 90
+
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