- PDB-4l0j: Structure of a translocation signal domain mediating conjugative ... -
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Basic information
Entry
Database: PDB / ID: 4l0j
Title
Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems
Components
DNA helicase IHelicase
Keywords
HYDROLASE / SH3 like domains / DNA binding
Function / homology
Function and homology information
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA helicase activity / DNA binding / ATP binding Similarity search - Function
DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase ...DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Method to determine structure: SAD / Resolution: 1.85→48.82 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.134 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22789
1506
5 %
RANDOM
Rwork
0.17819
-
-
-
obs
0.1807
28381
99.98 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 34.167 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.21 Å2
0 Å2
0 Å2
2-
-
0.21 Å2
0 Å2
3-
-
-
-0.42 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→48.82 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1661
0
9
107
1777
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.019
1696
X-RAY DIFFRACTION
r_angle_refined_deg
2.253
1.972
2304
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.589
5
215
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.887
22.533
75
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.779
15
264
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.582
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.168
0.2
262
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
1288
X-RAY DIFFRACTION
r_rigid_bond_restr
8.874
3
1694
X-RAY DIFFRACTION
r_sphericity_free
19.833
5
33
X-RAY DIFFRACTION
r_sphericity_bonded
18.586
5
1744
LS refinement shell
Resolution: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.298
129
-
Rwork
0.231
2063
-
obs
-
-
100 %
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