- PDB-4ffm: PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ffm
Title
PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)
Components
PylC
Keywords
LIGASE/PRODUCT / amino acid / biosynthesis of pyrrolysine / isopeptide bond formation / ATP-grasp fold / Ligase / ATP-binding / L-lysine and 3R-methyl-D-ornithine / Cytosol / LIGASE-PRODUCT complex
Function / homology
Function and homology information
3-methyl-D-ornithine-L-lysine ligase / pyrrolysine biosynthetic process / ligase activity / amino acid biosynthetic process / ATP binding / metal ion binding Similarity search - Function
Resolution: 1.9→2 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.4 / % possible all: 92.1
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Processing
Software
Name
Classification
XDS
datascaling
REFMAC
refinement
XDS
datareduction
XSCALE
datascaling
REFMAC
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→10 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.739 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20481
1355
5 %
RANDOM
Rwork
0.1636
-
-
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all
0.169
25744
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obs
0.1657
25744
99.74 %
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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: 37.413 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.51 Å2
0 Å2
0 Å2
2-
-
1.51 Å2
0 Å2
3-
-
-
-3.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.91→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2733
0
78
230
3041
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.02
2884
X-RAY DIFFRACTION
r_angle_refined_deg
1.673
2.017
3888
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.591
5
340
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.129
24.39
123
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.181
15
498
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.754
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
429
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2110
X-RAY DIFFRACTION
r_rigid_bond_restr
2.249
3
2884
X-RAY DIFFRACTION
r_sphericity_free
30.817
5
55
X-RAY DIFFRACTION
r_sphericity_bonded
12.182
5
2986
LS refinement shell
Resolution: 1.906→1.954 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.27
86
-
Rwork
0.219
1584
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obs
-
-
98.58 %
Refinement TLS params.
Method: refined / Origin x: 14.808 Å / Origin y: 4.984 Å / Origin z: 26.103 Å
11
12
13
21
22
23
31
32
33
T
0.0165 Å2
-0.0021 Å2
-0.0036 Å2
-
0.0075 Å2
0.0021 Å2
-
-
0.0032 Å2
L
0.0876 °2
0.0077 °2
0.0118 °2
-
0.1326 °2
0.0255 °2
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-
0.1061 °2
S
-0.0165 Å °
0.0053 Å °
-0.0066 Å °
0.005 Å °
0.0248 Å °
0.0079 Å °
0.0211 Å °
0.0133 Å °
-0.0083 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 363
2
X-RAY DIFFRACTION
1
A
901 - 905
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