LIGASE / Class ii aars and biotin synthetases fold / sufe/nifu fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information
lipoate-protein ligase activity / lipoate-protein ligase / protein lipoylation / ATP binding Similarity search - Function
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 / Enolase-like; domain 1 ...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 / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.99→29.1 Å / Num. obs: 25714 / % possible obs: 99.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 31.75 Å2 / Rsym value: 0.133 / Net I/σ(I): 14.2
Reflection shell
Resolution: 1.99→2.1 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 3632 / Rsym value: 0.717 / % possible all: 98.8
-
Processing
Software
Name
Version
Classification
XDS
datascaling
SCALA
4.2)
datascaling
SHARP
phasing
REFMAC
refinement
XDS
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MAD / Resolution: 1.99→29.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.554 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.153 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DISORDERED REGION (RESIDUES OF 172 AND 178) HAS BEEN MODELED USING XPLEO PROGRAM (H. VAN DEN BEDEM ET AL. ACTA CRYST. (2005) D61, 2-13) ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DISORDERED REGION (RESIDUES OF 172 AND 178) HAS BEEN MODELED USING XPLEO PROGRAM (H. VAN DEN BEDEM ET AL. ACTA CRYST. (2005) D61, 2-13) 3. THE ADDITIONAL DENSITY NEAR GLU170 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND, COVALENTLY BOUND TO THE RESIDUE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21691
1304
5.1 %
RANDOM
Rwork
0.15913
-
-
-
obs
0.16211
24363
99.77 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 30.181 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
0 Å2
2-
-
0.03 Å2
0 Å2
3-
-
-
-0.05 Å2
Refinement step
Cycle: LAST / Resolution: 1.99→29.1 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2578
0
73
284
2935
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2704
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2476
X-RAY DIFFRACTION
r_angle_refined_deg
1.53
1.956
3629
X-RAY DIFFRACTION
r_angle_other_deg
0.855
3
5712
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.664
5
331
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.669
24.846
130
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.039
15
446
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.708
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
407
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2998
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
552
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
512
X-RAY DIFFRACTION
r_nbd_other
0.188
0.2
2529
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1593
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.151
0.2
243
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.193
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.251
0.2
43
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.198
0.2
14
X-RAY DIFFRACTION
r_mcbond_it
2.275
3
1706
X-RAY DIFFRACTION
r_mcbond_other
0.584
3
680
X-RAY DIFFRACTION
r_mcangle_it
3.107
5
2643
X-RAY DIFFRACTION
r_scbond_it
5.304
8
1152
X-RAY DIFFRACTION
r_scangle_it
6.743
11
986
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
1304
LS refinement shell
Resolution: 1.99→2.042 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.305
104
5.75 %
Rwork
0.221
1704
-
obs
-
-
97.47 %
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
1.9355
0.3212
0.6755
1.3659
-0.1109
1.7203
-0.0004
0.0106
0.1958
0.1603
0.0124
0.1833
-0.1534
-0.1475
-0.012
-0.1422
0.0227
0.0057
-0.1329
-0.0047
-0.1098
9.2343
32.9398
15.7997
2
4.0885
1.3471
-2.1341
1.2907
-0.3434
2.7433
0.0902
0.2
0.4485
-0.0387
0.0624
0.2417
-0.3919
-0.2802
-0.1526
-0.0908
0.0469
-0.0295
0.0515
0.0464
-0.0413
0.2547
36.8856
4.1396
3
1.2752
0.0907
-0.3493
3.5031
-2.1856
7.5749
-0.0367
0.1914
-0.109
-0.002
-0.0625
-0.3011
0.3148
0.5788
0.0992
-0.2041
0.0236
-0.027
-0.1369
-0.0041
-0.0878
23.5959
24.1655
12.6902
4
2.588
-0.0943
1.7273
3.0446
-0.3702
3.4068
-0.0507
-0.126
0.0882
0.3481
-0.1342
-0.1514
-0.1052
0.124
0.1849
-0.0437
-0.0352
-0.0236
-0.1795
0.0179
-0.1653
22.8008
37.0607
37.5242
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
0 - 178
12 - 190
2
2
179 - 215
191 - 227
3
3
216 - 245
228 - 257
4
4
246 - 329
258 - 341
+
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