- PDB-3pdg: Structures of Clostridium thermocellum CbhA fibronectin(III)-like... -
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Basic information
Entry
Database: PDB / ID: 3pdg
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
Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulase activity / 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
Resolution: 1.78→1.88 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 2.72 / Num. unique all: 1573 / Rsym value: 0.2817 / % possible all: 98.9
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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: SIRAS / Resolution: 1.78→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.802 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2705
518
4.8 %
RANDOM
Rwork
0.23017
-
-
-
obs
0.23217
10241
99.17 %
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all
-
10241
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-
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: 25.68 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.2 Å2
0 Å2
0 Å2
2-
-
1.2 Å2
0 Å2
3-
-
-
-2.4 Å2
Refinement step
Cycle: LAST / Resolution: 1.78→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
669
0
2
93
764
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
732
X-RAY DIFFRACTION
r_bond_other_d
0.011
0.02
478
X-RAY DIFFRACTION
r_angle_refined_deg
1.98
1.985
1007
X-RAY DIFFRACTION
r_angle_other_deg
0.979
3
1190
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.648
5
102
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.74
24.091
22
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.268
15
125
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.876
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
127
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
833
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
135
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
1.025
1.5
490
X-RAY DIFFRACTION
r_mcbond_other
0.391
1.5
194
X-RAY DIFFRACTION
r_mcangle_it
1.538
2
811
X-RAY DIFFRACTION
r_scbond_it
2.936
3
242
X-RAY DIFFRACTION
r_scangle_it
4.22
4.5
196
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.78→1.826 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.401
44
-
Rwork
0.308
686
-
obs
-
730
93.83 %
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
2.5003
0.1696
-0.9193
2.2
-1.4595
6.9311
-0.0996
0.1993
-0.057
-0.1728
0.0488
-0.0784
0.1394
-0.1098
0.0508
0.1021
-0.0008
-0.0097
0.0963
-0.0094
0.1218
-19.8059
-13.8742
-21.5958
2
2.5238
0.9151
-1.1185
1.1384
1.3338
4.5111
-0.0001
0.1335
0.134
-0.165
0.0292
0.0344
-0.1878
-0.0326
-0.0291
0.1657
0.0103
-0.0099
0.1815
0.0081
0.1751
-12.4502
-4.3694
-30.8961
3
2.6674
0.3732
-2.0055
0.9416
-0.6383
3.688
-0.0514
-0.0308
-0.0755
-0.0562
0.0387
-0.0645
0.0095
0.0227
0.0126
0.1142
0.0129
-0.0119
0.0654
-0.0077
0.1124
-18.1951
-9.9884
-11.6557
4
0.3933
0.625
0.0694
1.6486
-0.1136
2.1944
0.0411
-0.1313
0.156
0.0985
-0.0274
0.0697
-0.1305
-0.0352
-0.0137
0.1291
-0.0003
0.0007
0.1555
-0.043
0.1698
-20.7878
-3.7743
-12.5302
5
2.3626
0.4037
-1.9597
0.9448
0.2563
2.4036
0.0841
0.1455
0.2413
-0.1538
-0.0154
-0.1057
-0.2895
-0.0523
-0.0687
0.1221
-0.0075
-0.0304
0.159
0.0307
0.2016
-9.2942
-5.8084
-23.3337
6
0.5264
0.1052
0.1694
1.1146
0.3065
0.2258
0.0049
-0.0134
0.1067
0.0267
-0.0016
-0.0317
-0.0822
0.0318
-0.0033
0.0831
-0.0238
0.02
0.0329
-0.0083
0.0316
-18.5661
-14.1076
-4.1231
7
1.5353
0.119
-2.2919
1.2605
-1.5566
8.1304
-0.0106
0.0042
0.0496
-0.0152
-0.0091
-0.0774
-0.0909
0.2026
0.0198
0.0848
-0.001
-0.0087
0.0841
-0.0064
0.1105
-13.3842
-15.5602
-17.3108
8
0.2248
0.0662
-0.3764
0.2131
-0.5198
1.6472
-0.0021
0.1401
-0.134
-0.1634
0.0348
0.08
0.3004
-0.1218
-0.0328
0.1939
0.0221
-0.0357
0.19
-0.0349
0.2275
-8.2163
-5.4904
-38.2226
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 10
2
X-RAY DIFFRACTION
2
A
11 - 19
3
X-RAY DIFFRACTION
3
A
20 - 42
4
X-RAY DIFFRACTION
4
A
43 - 52
5
X-RAY DIFFRACTION
5
A
53 - 66
6
X-RAY DIFFRACTION
6
A
67 - 75
7
X-RAY DIFFRACTION
7
A
76 - 85
8
X-RAY DIFFRACTION
8
A
86 - 91
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