- PDB-3pdd: Structures of Clostridium thermocellum CbhA fibronectin(III)-like... -
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Basic information
Entry
Database: PDB / ID: 3pdd
Title
Structures of Clostridium thermocellum CbhA fibronectin(III)-like modules
Components
Glycoside hydrolase, family 9
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: 1.72→1.81 Å / Redundancy: 5.24 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3291 / Rsym value: 0.6206 / % possible all: 100
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Processing
Software
Name
Version
Classification
PROTEUM PLUS
datacollection
MOLREP
phasing
REFMAC
5.5.0109
refinement
SAINT
datareduction
PROTEUM PLUS
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→23.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.155 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22639
1208
5.1 %
RANDOM
Rwork
0.16664
-
-
-
obs
0.16959
22264
99.76 %
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all
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22264
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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: 16.365 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
-0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.72→23.94 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1448
0
5
501
1954
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
1603
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1073
X-RAY DIFFRACTION
r_angle_refined_deg
1.792
1.954
2203
X-RAY DIFFRACTION
r_angle_other_deg
0.927
3
2661
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.466
5
221
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.601
24.559
68
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.579
15
281
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.572
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.122
0.2
255
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
1835
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
308
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
1.079
1.5
1014
X-RAY DIFFRACTION
r_mcbond_other
0.403
1.5
403
X-RAY DIFFRACTION
r_mcangle_it
1.67
2
1671
X-RAY DIFFRACTION
r_scbond_it
2.776
3
589
X-RAY DIFFRACTION
r_scangle_it
4.291
4.5
520
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.72→1.764 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.353
93
-
Rwork
0.318
1588
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obs
-
93
99.12 %
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
1.1537
-0.1267
-0.6036
0.7094
-0.0355
1.7783
-0.0261
0.0098
-0.0619
0.001
0.0173
0.0516
0.0938
-0.0872
0.0089
0.0314
0.0026
-0.0167
0.0265
-0.0079
0.0432
-1.7367
-15.3936
30.5584
2
0.9458
-0.2463
0.8014
0.6156
-0.2797
1.0921
0.0183
0.0405
-0.041
-0.06
-0.0053
-0.0137
0.0886
0.0597
-0.013
0.0237
-0.0046
0.0166
0.0243
-0.0058
0.0356
-7.07
-4.3883
-10.596
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 88
2
X-RAY DIFFRACTION
2
A
89 - 190
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