DIPHTHERIATOXIN / DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN ...DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN FRAGMENT B / CRM197
Mass: 58483.422 Da / Num. of mol.: 1 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) CORYNEBACTERIUM DIPHTHERIAE (bacteria) References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, GLY 53 TO GLU
Sequence details
COORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE ...COORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE NATURAL GLY TO GLU MUTATION AT POSITION 52 INSTEAD OF 53. RESIDUES 1-32 IN THE UNIPROT SEQUENCE ARE THE SIGNAL PEPTIDE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal grow
pH: 9 / Details: 1.9 M AMMONIUM SULFATE, 100 MM BICINE [PH 9.0]
Resolution: 1.996→41.335 Å / SU ML: 0.29 / σ(F): 0.21 / Phase error: 28.36 / Stereochemistry target values: ML Details: RESIDUES 1-4, 38-49, 188-200, 349-352, AND 517-519, ARE DISORDERED. DISORDERED SIDE CHAINS WERE MODELED UP TO THE BACKBONE CBETA ATOMS, AND RESIDUE NAMES WERE KEPT CONSISTENT WITH SEQUENCE OF THE PROTEIN.
Rfactor
Num. reflection
% reflection
Rfree
0.2411
1837
5 %
Rwork
0.2096
-
-
obs
0.2112
36533
88.51 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.666 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Biso mean: 56 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-8.2649 Å2
0 Å2
-9.5035 Å2
2-
-
15.4835 Å2
0 Å2
3-
-
-
-7.2187 Å2
Refinement step
Cycle: LAST / Resolution: 1.996→41.335 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3664
0
0
169
3833
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3735
X-RAY DIFFRACTION
f_angle_d
0.961
5082
X-RAY DIFFRACTION
f_dihedral_angle_d
12.271
1287
X-RAY DIFFRACTION
f_chiral_restr
0.067
590
X-RAY DIFFRACTION
f_plane_restr
0.004
664
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9958-2.0671
0.305
96
0.2699
2137
X-RAY DIFFRACTION
55
2.0671-2.1499
0.3065
163
0.2466
2985
X-RAY DIFFRACTION
77
2.1499-2.2477
0.2805
173
0.2238
3318
X-RAY DIFFRACTION
85
2.2477-2.3662
0.2433
176
0.2123
3463
X-RAY DIFFRACTION
89
2.3662-2.5145
0.2843
186
0.2149
3605
X-RAY DIFFRACTION
92
2.5145-2.7086
0.2586
204
0.2135
3735
X-RAY DIFFRACTION
95
2.7086-2.9811
0.2735
190
0.2175
3829
X-RAY DIFFRACTION
97
2.9811-3.4123
0.2435
212
0.2202
3870
X-RAY DIFFRACTION
99
3.4123-4.2984
0.2122
211
0.1885
3906
X-RAY DIFFRACTION
99
4.2984-41.3437
0.2216
226
0.1927
3848
X-RAY DIFFRACTION
97
Refinement TLS params.
Method: refined / Origin x: -15.9226 Å / Origin y: 24.0845 Å / Origin z: 27.364 Å
11
12
13
21
22
23
31
32
33
T
0.279 Å2
-0.0234 Å2
0.0243 Å2
-
0.3515 Å2
0.0245 Å2
-
-
0.262 Å2
L
1.137 °2
0.177 °2
-0.0665 °2
-
1.0249 °2
0.1043 °2
-
-
0.4686 °2
S
-0.1805 Å °
0.1049 Å °
0.0038 Å °
-0.1289 Å °
0.1524 Å °
0.1927 Å °
-0.0506 Å °
-0.1535 Å °
0.0253 Å °
Refinement TLS group
Selection details: ALL
+
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