BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS NOT CLEAR.
Remark 400
COMPOUND THE AUTHORS STATE THE FOLLOWING: BASED ON THE PROTEIN SEQUENCE, THIS PROTEIN, AQ_TRMD, IS ...COMPOUND THE AUTHORS STATE THE FOLLOWING: BASED ON THE PROTEIN SEQUENCE, THIS PROTEIN, AQ_TRMD, IS ANNOTATED AS A TRNA (M1G37) METHYLTRANSFERASE, SAME AS ANOTHER TRNA (M1G37) METHYLTRANSFERASE OF KNOWN STRUCTURE (SUCH AS 1UAJ, 1UAK, 1UAL, 1UAM). THE MAJOR DIFFERENCE IS THAT THE LATTER STRUCTURES HAVE "TRIFOIL KNOTS", WHICH IS PROPOSED AS ESSENTIAL FOR S-ADENOSYL-L-METHIONINE BINDING, WHILE THIS STRUCTURE DOES NOT HAVE THE KNOT. THEREFORE, IT IS POSSIBLE THAT THE PROTEIN IN THIS ENTRY MAY HAVE A BIOCHEMICAL FUNCTION DIFFERENT FROM TRNA (1MG37) METHYLTRANSFERASE DESPITE THE SEQUENCE-BASED ANNOTATION AS SUCH.
Method to determine structure: MAD / Resolution: 2.6→20 Å / SU B: 20.353 / SU ML: 0.454 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.086 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.30029
1312
5.2 %
RANDOM
Rwork
0.27937
-
-
-
obs
0.28048
24034
99.35 %
-
all
-
24191
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 29.025 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.75 Å2
0 Å2
0.16 Å2
2-
-
1.89 Å2
0 Å2
3-
-
-
-1.1 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5303
0
0
76
5379
LS refinement shell
Resolution: 2.6→2.666 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.343
90
Rwork
0.298
1734
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
2.5478
0.5433
-0.6714
4.4106
0.2262
4.9878
-0.2551
-0.0388
-0.1883
0.0163
0.2507
-0.3595
0.2735
0.3899
0.0044
0.0666
0.0124
-0.0099
0.1279
-0.0875
0.1293
-37.5218
-10.192
9.4359
2
4.1335
-0.6957
0.8279
1.505
0.1464
3.927
0.0042
-0.096
0.0696
-0.0264
-0.0145
0.001
-0.0095
0.0265
0.0103
0.055
-0.0103
0.0013
0.0545
0.0043
0.0294
-14.3445
42.2779
24.2227
3
4.1294
2.1136
-1.3969
5.7814
-1.0157
3.6675
-0.0354
-0.2038
0.0383
-0.2687
-0.0343
-0.5903
-0.0397
0.1815
0.0696
0.1551
-0.0905
0.001
0.1425
-0.1462
0.2362
-25.3947
10.2309
4.8704
4
13.2934
0.5164
2.2644
6.5572
-2.5674
9.1935
-0.2886
0.5279
-2.4543
-1.2192
-0.3898
-1.4608
1.8869
1.0217
0.6784
1.0256
-0.166
0.7649
0.552
-0.1537
1.3512
-9.614
5.791
-9.9538
5
8.8721
-0.8664
3.2591
9.6893
-1.3787
3.1473
0.1145
-0.5782
1.6154
0.4607
-0.2011
0.9953
-0.9943
0.3086
0.0867
0.4929
-0.2334
0.1856
0.3624
-0.2241
0.5112
8.5896
57.6801
48.8469
6
18.5065
-3.7492
-4.2862
4.4409
4.2074
-1.0641
-0.813
-0.7501
0.3196
0.9449
0.9271
-1.0207
1.3593
0.4979
-0.1141
1.1212
0.5794
-0.3177
0.5548
0.0003
0.53
-26.7051
-20.3982
25.9528
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
4 - 164
4 - 164
2
X-RAY DIFFRACTION
2
B
B
304 - 464
4 - 164
3
X-RAY DIFFRACTION
3
C
C
604 - 764
4 - 164
4
X-RAY DIFFRACTION
4
A
A
179 - 235
179 - 235
5
X-RAY DIFFRACTION
5
B
B
479 - 535
179 - 235
6
X-RAY DIFFRACTION
6
C
C
779 - 835
179 - 235
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
bond_d
0.018
X-RAY DIFFRACTION
angle_d
X-RAY DIFFRACTION
angle_deg
1.97
+
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