DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function
DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. ...DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Method to determine structure: OTHER Starting model: NONE Resolution: 2.94→30.44 Å / Cor.coef. Fo:Fc: 0.9051 / Cor.coef. Fo:Fc free: 0.8493 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.401 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2563
1012
5.06 %
RANDOM
Rwork
0.1953
-
-
-
obs
0.1984
20004
99.71 %
-
Displacement parameters
Biso mean: 49.38 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.2479 Å2
0 Å2
-2.3384 Å2
2-
-
8.1216 Å2
0 Å2
3-
-
-
-13.3695 Å2
Refine analyze
Luzzati coordinate error obs: 0.346 Å
Refinement step
Cycle: LAST / Resolution: 2.94→30.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5875
0
256
18
6149
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
6253
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.25
8558
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2195
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
166
HARMONIC
8
X-RAY DIFFRACTION
t_gen_planes
979
HARMONIC
8
X-RAY DIFFRACTION
t_it
6253
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
1.86
X-RAY DIFFRACTION
t_other_torsion
20.53
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
873
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
7255
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.94→3.1 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.2851
135
4.63 %
Rwork
0.2162
2780
-
all
0.2195
2915
-
obs
-
-
99.71 %
+
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