- PDB-7quz: Crystal structure of the SeMet octameric C-terminal Big_2-CBM56 d... -
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Basic information
Entry
Database: PDB / ID: 7quz
Title
Crystal structure of the SeMet octameric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H
hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function
: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Invasin/intimin cell-adhesion fragments / Glycosyl hydrolases family 16 / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. ...: / CBM56 (carbohydrate binding type-56) domain profile. / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Invasin/intimin cell-adhesion fragments / Glycosyl hydrolases family 16 / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Concanavalin A-like lectin/glucanase domain superfamily Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein concentration 30.0 mg/ml, 0.1 M Magnesium Chloride hexahydrate, 0.1 M HEPES pH 7.5, PEG 400 with 30% glycerol added to crystallisation buffer for cryocooling.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Method to determine structure: SAD / Resolution: 2.156→48.771 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.895 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.274 / ESU R Free: 0.232 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2924
4797
5.093 %
Rwork
0.2397
89388
-
all
0.242
-
-
obs
-
94185
99.747 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 26.918 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.99 Å2
-0 Å2
-0.732 Å2
2-
-
-0.491 Å2
-0 Å2
3-
-
-
-0.433 Å2
Refinement step
Cycle: LAST / Resolution: 2.156→48.771 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10726
0
60
796
11582
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
11058
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
10146
X-RAY DIFFRACTION
r_angle_refined_deg
1.766
1.648
15223
X-RAY DIFFRACTION
r_angle_other_deg
1.27
1.571
23356
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.66
5
1479
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.034
26.667
420
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.483
15
1471
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
1562
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
13038
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2338
X-RAY DIFFRACTION
r_nbd_refined
0.189
0.2
1708
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.186
0.2
8840
X-RAY DIFFRACTION
r_nbtor_refined
0.162
0.2
5119
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.078
0.2
5438
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.178
0.2
612
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.044
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.196
0.2
99
X-RAY DIFFRACTION
r_nbd_other
0.253
0.2
245
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.205
0.2
57
X-RAY DIFFRACTION
r_mcbond_it
0.814
1.454
5910
X-RAY DIFFRACTION
r_mcbond_other
0.814
1.453
5909
X-RAY DIFFRACTION
r_mcangle_it
1.465
2.173
7376
X-RAY DIFFRACTION
r_mcangle_other
1.465
2.173
7377
X-RAY DIFFRACTION
r_scbond_it
0.874
1.536
5145
X-RAY DIFFRACTION
r_scbond_other
0.874
1.537
5146
X-RAY DIFFRACTION
r_scangle_it
1.451
2.273
7842
X-RAY DIFFRACTION
r_scangle_other
1.451
2.273
7843
X-RAY DIFFRACTION
r_lrange_it
4.042
17.641
11201
X-RAY DIFFRACTION
r_lrange_other
3.974
17.46
11068
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.156-2.212
0.444
347
0.444
6322
X-RAY DIFFRACTION
97.2016
2.212-2.272
0.406
361
0.393
6387
X-RAY DIFFRACTION
99.9408
2.272-2.338
0.388
324
0.36
6264
X-RAY DIFFRACTION
100
2.338-2.41
0.374
306
0.348
6057
X-RAY DIFFRACTION
99.9372
2.41-2.489
0.391
339
0.336
5859
X-RAY DIFFRACTION
100
2.489-2.577
0.396
287
0.308
5689
X-RAY DIFFRACTION
99.9833
2.577-2.674
0.35
281
0.285
5504
X-RAY DIFFRACTION
100
2.674-2.783
0.31
287
0.246
5269
X-RAY DIFFRACTION
99.964
2.783-2.907
0.303
267
0.231
5113
X-RAY DIFFRACTION
100
2.907-3.049
0.255
254
0.212
4895
X-RAY DIFFRACTION
99.9806
3.049-3.214
0.283
235
0.196
4611
X-RAY DIFFRACTION
100
3.214-3.408
0.263
242
0.194
4379
X-RAY DIFFRACTION
100
3.408-3.644
0.263
202
0.196
4140
X-RAY DIFFRACTION
100
3.644-3.935
0.259
218
0.193
3823
X-RAY DIFFRACTION
100
3.935-4.311
0.231
227
0.161
3565
X-RAY DIFFRACTION
100
4.311-4.819
0.161
180
0.129
3176
X-RAY DIFFRACTION
100
4.819-5.564
0.188
149
0.157
2865
X-RAY DIFFRACTION
99.9337
5.564-6.813
0.268
127
0.168
2445
X-RAY DIFFRACTION
100
6.813-9.627
0.226
115
0.151
1902
X-RAY DIFFRACTION
99.9504
9.627-48.771
0.249
49
0.205
1117
X-RAY DIFFRACTION
98.9813
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
1.2953
-0.5433
-1.8631
0.5627
0.7844
3.2774
0.0063
-0.1403
0.0868
0.0595
0.0857
-0.1199
-0.0008
0.2308
-0.092
0.1585
-0.0013
0.0783
0.0189
-0.0182
0.0873
9.5447
-25.3583
1.1741
2
0.6711
-0.3102
-1.1816
0.5903
0.732
3.5814
-0.0528
-0.0996
0.0109
0.0717
0.1108
-0.1333
0.2398
0.2596
-0.058
0.176
0.025
0.0647
0.0266
-0.017
0.0761
7.4584
-46.9518
6.21
3
1.1609
0.4334
-1.7789
0.573
-0.7621
3.362
-0.0033
0.1119
0.0626
-0.0753
0.0724
0.1129
0.0309
-0.226
-0.0692
0.151
-0.0018
0.0617
0.0194
0.0118
0.0702
-13.1778
-51.3751
82.6879
4
0.8018
0.287
-1.2761
0.7976
-0.7415
3.4509
-0.0475
0.1353
-0.021
-0.0756
0.0839
0.1715
0.2514
-0.2649
-0.0365
0.2042
-0.026
0.0766
0.0262
-0
0.092
-10.8632
-72.901
77.4537
5
0.6696
-0.3608
-0.8267
0.8294
1.1152
3.6385
-0.017
-0.0708
0.0929
0.0191
0.0999
-0.1138
-0.1592
0.281
-0.083
0.1333
-0.0372
0.0928
0.0644
-0.0083
0.1428
-42.0364
-83.538
41.9557
6
0.6731
0.1091
-0.5294
0.7258
-0.799
3.8764
0.0344
0.1033
-0.0324
-0.0653
0.1394
0.1684
0.2463
-0.2742
-0.1738
0.144
-0.0258
0.0806
0.0717
-0.017
0.1608
-60.4408
-105.0812
39.4412
7
0.8734
0.2378
-1.0282
0.8145
-0.7783
3.683
-0.0061
0.0487
0.0717
-0.0072
0.0922
0.1272
-0.0995
-0.2508
-0.0862
0.1058
0.027
0.0854
0.0384
0.0098
0.1629
-61.1436
-83.5314
44.3837
8
0.6214
0.0094
-0.5075
0.7853
0.9552
4.6732
-0.0184
-0.0712
0.0288
0.111
0.1012
-0.1862
0.2473
0.2459
-0.0828
0.1423
0.0472
0.0722
0.0416
0.0074
0.1664
-42.7708
-104.9927
47.0346
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
AAA
24 - 207
2
X-RAY DIFFRACTION
2
ALL
BBB
22 - 207
3
X-RAY DIFFRACTION
3
ALL
CCC
24 - 207
4
X-RAY DIFFRACTION
4
ALL
DDD
21 - 207
5
X-RAY DIFFRACTION
5
ALL
EEE
24 - 207
6
X-RAY DIFFRACTION
6
ALL
FFF
24 - 207
7
X-RAY DIFFRACTION
7
ALL
GGG
24 - 207
8
X-RAY DIFFRACTION
8
ALL
HHH
24 - 207
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