lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / ATP binding / cytoplasm / cytosol Similarity search - Function
Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.9→3 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2939 / % possible all: 99
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: Difference Fourier Starting model: Lipoate protein ligase A from E. coli Resolution: 2.91→66.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.859 / SU B: 15.864 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2714
1533
5.3 %
RANDOM
Rwork
0.1863
-
-
-
all
0.1907
27666
-
-
obs
0.1907
27666
97.1 %
-
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: 39.469 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.59 Å2
0 Å2
0 Å2
2-
-
-0.05 Å2
0 Å2
3-
-
-
-0.54 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.303 Å
0.435 Å
Refinement step
Cycle: LAST / Resolution: 2.91→66.67 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7891
0
24
22
7937
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.02
0.022
8084
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.976
1.948
10951
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.038
5
992
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.855
23.596
406
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.67
15
1344
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.997
15
73
X-RAY DIFFRACTION
r_chiral_restr
0.119
0.2
1196
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
6240
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.254
0.2
3992
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.329
0.2
5509
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.169
0.2
329
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
0.195
0.2
76
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.169
0.2
7
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
0.845
1.5
5048
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.467
2
7946
X-RAY DIFFRACTION
r_scbond_it
2.238
3
3394
X-RAY DIFFRACTION
r_scangle_it
3.692
4.5
3005
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Highest resolution: 2.91 Å / Num. reflection Rwork: 1955 / Total num. of bins used: 20
+
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