- PDB-7ybd: Crystal structure of sliding DNA clamp of Clostridioides difficile -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7ybd
Title
Crystal structure of sliding DNA clamp of Clostridioides difficile
Components
Beta sliding clamp
Keywords
DNA BINDING PROTEIN / DNA replication
Function / homology
Function and homology information
DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function
DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→41.452 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.632 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.201 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2392
1095
-
Rwork
0.1786
20287
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all
0.182
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-
obs
-
21382
98.453 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parameters
Biso mean: 44.552 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.133 Å2
0 Å2
0.015 Å2
2-
-
0.083 Å2
0 Å2
3-
-
-
-0.148 Å2
Refinement step
Cycle: LAST / Resolution: 2.13→41.452 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2863
0
10
145
3018
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.012
2904
X-RAY DIFFRACTION
r_angle_refined_deg
1.519
1.63
3917
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.456
5
357
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.341
24.69
145
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.367
15
569
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.969
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.119
0.2
409
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2108
X-RAY DIFFRACTION
r_nbd_refined
0.234
0.2
1267
X-RAY DIFFRACTION
r_nbtor_refined
0.314
0.2
2007
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.2
163
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.248
0.2
43
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.216
0.2
7
X-RAY DIFFRACTION
r_mcbond_it
3.323
4.09
1437
X-RAY DIFFRACTION
r_mcangle_it
4.849
6.112
1791
X-RAY DIFFRACTION
r_scbond_it
4.863
4.678
1467
X-RAY DIFFRACTION
r_scangle_it
7.397
6.769
2126
X-RAY DIFFRACTION
r_lrange_it
9.161
56.346
4343
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.13-2.185
0.331
79
0.266
1484
X-RAY DIFFRACTION
97.6265
2.185-2.245
0.33
65
0.247
1431
X-RAY DIFFRACTION
98.0984
2.245-2.31
0.257
84
0.235
1412
X-RAY DIFFRACTION
98.0984
2.31-2.381
0.272
83
0.221
1363
X-RAY DIFFRACTION
98.4343
2.381-2.459
0.312
73
0.213
1286
X-RAY DIFFRACTION
97.8402
2.459-2.545
0.254
76
0.225
1311
X-RAY DIFFRACTION
98.5785
2.545-2.641
0.296
77
0.22
1247
X-RAY DIFFRACTION
98.3655
2.641-2.748
0.29
70
0.203
1182
X-RAY DIFFRACTION
97.889
2.748-2.87
0.296
63
0.21
1132
X-RAY DIFFRACTION
98.5161
2.87-3.01
0.275
62
0.193
1096
X-RAY DIFFRACTION
98.8898
3.01-3.172
0.224
57
0.185
1061
X-RAY DIFFRACTION
98.6761
3.172-3.363
0.203
56
0.165
986
X-RAY DIFFRACTION
98.8615
3.363-3.594
0.223
46
0.16
937
X-RAY DIFFRACTION
98.497
3.594-3.881
0.212
35
0.158
892
X-RAY DIFFRACTION
99.4635
3.881-4.248
0.215
39
0.154
808
X-RAY DIFFRACTION
98.4884
4.248-4.746
0.168
23
0.128
756
X-RAY DIFFRACTION
99.4891
4.746-5.472
0.173
42
0.153
644
X-RAY DIFFRACTION
99.2764
5.472-6.681
0.242
34
0.19
559
X-RAY DIFFRACTION
99.33
6.681-9.366
0.245
16
0.141
441
X-RAY DIFFRACTION
99.3478
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