- PDB-4q6l: LpoB C-terminal domain from Salmonella enterica (Native) -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4q6l
Title
LpoB C-terminal domain from Salmonella enterica (Native)
Components
Penicillin-binding protein activator LpoB
Keywords
PROTEIN BINDING / mixed alpha-beta / Lipoprotein / Activator of PBP1b / PBP1b / lipidation / outer-membrane
Function / homology
Function and homology information
periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / regulation of cell shape Similarity search - Function
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.2 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.849 / SU B: 27.79 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29685
266
4.5 %
RANDOM
Rwork
0.24872
-
-
-
obs
0.25093
5584
99.25 %
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all
-
5612
-
-
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: 33.831 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.74 Å2
0 Å2
0 Å2
2-
-
2.72 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→49.2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
995
0
0
12
1007
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.019
1026
X-RAY DIFFRACTION
r_angle_refined_deg
1.454
1.952
1392
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.095
5
138
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.163
26.279
43
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.119
15
179
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.896
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
163
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
768
X-RAY DIFFRACTION
r_mcbond_it
3.441
2.756
549
X-RAY DIFFRACTION
r_mcangle_it
4.058
4.121
688
X-RAY DIFFRACTION
r_scbond_it
4.794
2.894
477
X-RAY DIFFRACTION
r_long_range_B_refined
4.973
35.552
4237
X-RAY DIFFRACTION
r_rigid_bond_restr
11.619
3
1026
X-RAY DIFFRACTION
r_sphericity_bonded
24.591
5
1014
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.347
26
-
Rwork
0.312
380
-
obs
-
-
97.36 %
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
0.1776
0.3774
0.3051
2.4457
0.4011
0.5916
0.2355
-0.118
0.1028
0.4482
-0.0996
0.1123
-0.0823
-0.092
-0.0099
0.4965
-0.0272
0.0638
0.1502
-0.0232
0.4492
-4.8072
6.9318
-8.9293
2
2.613
-0.1293
0.6983
3.2834
0.0611
2.558
-0.0121
0.226
-0.1618
0.0335
0.0769
-0.0908
0.2536
0.1845
-0.0285
0.3457
0.037
-0.002
0.1042
0.0099
0.3378
-9.1565
17.2828
-20.1284
3
0.4894
0.372
0.1713
1.4262
0.4588
0.4239
0.1413
-0.0557
0.1061
0.2053
0.0031
-0.0968
0.0014
0.0203
0.2414
0.4199
-0.076
0.0191
0.0211
-0.0722
0.3105
0.3452
5.9469
-14.3685
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
chainAand ( resid78through131 )
A
78 - 131
2
X-RAY DIFFRACTION
2
chainAand ( resid132through170 )
A
132 - 170
3
X-RAY DIFFRACTION
3
chainAand ( resid171through211 )
A
171 - 211
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