Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Sequence details
CRYSTALLIZED PROTEIN CONTAINS ADDITIONAL N-TERMINAL HISTIDINE TAG AND LINKER HHHHHHGS. ...CRYSTALLIZED PROTEIN CONTAINS ADDITIONAL N-TERMINAL HISTIDINE TAG AND LINKER HHHHHHGS. ADDITIONALLY, ALL METHIONINE RESIDUES WERE DERIVATISED INTO SELENO- METHIONINE RESIDUES. THIS SE-MET UGDG PROTEIN STRUCTURE CORRESPONDS TO THE SE-MET DERIVATIZED DNA SEQUENCE OF GENBANK ENTRY EF488145.2, WHERE UGDG CORRESPONDS TO NUCLEOTIDES 1359-2675. UGDG THUS BEGINS WITH NUCLEOTIDES 1359-13560-13561, WHICH FORM THE CODON GTG. THE CANONICAL TRANSLATION OF CODON GTG IS VALINE, AS IN THE PRESENT STRUCTURE.ODDLY, IN ITS GENBANK ENTRY THE GTG FIRST CODON OF UGDG WAS WRONGLY TRANSLATED INTO METHIONINE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.65 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 1 ML DROPS OF PROTEIN SOLUTION, 5.5 MG/ML SE-MET UGDG IN 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT AND 1 MM NAD, WERE MIXED WITH 1 ML DROPS OF PRECIPITANT SOLUTION, 0.1 M MES PH 6.5, 40 ...Details: 1 ML DROPS OF PROTEIN SOLUTION, 5.5 MG/ML SE-MET UGDG IN 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT AND 1 MM NAD, WERE MIXED WITH 1 ML DROPS OF PRECIPITANT SOLUTION, 0.1 M MES PH 6.5, 40 % (W/V) PEG 200, AND LET EQUILIBRATE BY VAPOR DIFFUSION AGAINST 500 ML PRECIPITANT SOLUTION AT 293 K.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.931 Å / Relative weight: 1
Reflection
Resolution: 3.4→48.78 Å / Num. obs: 27657 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 121.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.1
Reflection shell
Resolution: 3.4→3.52 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5
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Processing
Software
Name
Classification
FFFEAR
modelbuilding
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
DM
phasing
RESOLVE
phasing
FFFEAR
phasing
XFIT
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 3.403→48.76 Å / SU ML: 0.91 / σ(F): 1.38 / Phase error: 21.28 / Stereochemistry target values: ML Details: SE-MET UGDG SAD PHASES LED TO A PRELIMINARY MODEL, WITH 346 OUT OF 438 RESIDUES OF WHICH 318 WERE ASSIGNED AS ALANINES, WHICH WAS USED FOR MOLECULAR REPLACEMENT OF A NATIVE UGDG HEXAGONAL ...Details: SE-MET UGDG SAD PHASES LED TO A PRELIMINARY MODEL, WITH 346 OUT OF 438 RESIDUES OF WHICH 318 WERE ASSIGNED AS ALANINES, WHICH WAS USED FOR MOLECULAR REPLACEMENT OF A NATIVE UGDG HEXAGONAL CRYSTAL THAT DIFFRACTED UP TO 2.15 ANGSTROM RESOLUTION. THE REFINED NATIVE UGDG HEXAGONAL MODEL WAS THEN USED WITH THE PRESENT SE-MET UGDG DATA TO REFINE THE HERE PRESENTED SE-MET UGDG STRUCTURE. THE SE-MET UGDG REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.2018 AND 0.2342, RESPECTIVELY, USING A THIN-SHELLS R-FREE SET WITH 1859 REFLECTIONS. THE FINAL SE-MET UGDG MODEL WAS THEN REFINED WEIGHTING THE STEREO-CHEMICAL AND ADP RESTRAINTS VERSUS THE FULL DATA SET IN ORDER TO OBTAIN BOND DISTANCES, ANGLES AND ADP RMSDS SIMILAR TO THOSE OBTAINED IN THE PRECEDENT R-FREE GUIDED REFINEMENT.
Rfactor
Num. reflection
% reflection
Rwork
0.2298
-
-
obs
-
27657
99.59 %
Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.669 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Biso mean: 130 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-10.0266 Å2
0 Å2
0 Å2
2-
-
-10.0266 Å2
0 Å2
3-
-
-
20.0532 Å2
Refinement step
Cycle: LAST / Resolution: 3.403→48.76 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6469
0
88
0
6557
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
6665
X-RAY DIFFRACTION
f_angle_d
1.011
9047
X-RAY DIFFRACTION
f_dihedral_angle_d
17.835
2456
X-RAY DIFFRACTION
f_chiral_restr
0.068
1055
X-RAY DIFFRACTION
f_plane_restr
0.005
1177
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
3260
X-RAY DIFFRACTION
POSITIONAL
1
2
B
3260
X-RAY DIFFRACTION
POSITIONAL
0.013
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.403-3.4417
0.2945
919
0.2945
919
X-RAY DIFFRACTION
99
3.4417-3.4822
0.3049
907
0.3049
907
X-RAY DIFFRACTION
100
3.4822-3.5246
0.312
929
0.312
929
X-RAY DIFFRACTION
100
3.5246-3.5692
0.273
918
0.273
918
X-RAY DIFFRACTION
100
3.5692-3.6162
0.2827
933
0.2827
933
X-RAY DIFFRACTION
100
3.6162-3.6657
0.2716
924
0.2716
924
X-RAY DIFFRACTION
100
3.6657-3.7181
0.2405
916
0.2405
916
X-RAY DIFFRACTION
100
3.7181-3.7735
0.2577
941
0.2577
941
X-RAY DIFFRACTION
100
3.7735-3.8325
0.2631
937
0.2631
937
X-RAY DIFFRACTION
100
3.8325-3.8953
0.2423
939
0.2423
939
X-RAY DIFFRACTION
100
3.8953-3.9624
0.2607
897
0.2607
897
X-RAY DIFFRACTION
100
3.9624-4.0345
0.2479
948
0.2479
948
X-RAY DIFFRACTION
100
4.0345-4.112
0.2321
899
0.2321
899
X-RAY DIFFRACTION
100
4.112-4.1959
0.2276
925
0.2276
925
X-RAY DIFFRACTION
100
4.1959-4.2871
0.2201
920
0.2201
920
X-RAY DIFFRACTION
100
4.2871-4.3867
0.2039
927
0.2039
927
X-RAY DIFFRACTION
100
4.3867-4.4964
0.2342
924
0.2342
924
X-RAY DIFFRACTION
100
4.4964-4.6179
0.2107
923
0.2107
923
X-RAY DIFFRACTION
100
4.6179-4.7536
0.2193
929
0.2193
929
X-RAY DIFFRACTION
100
4.7536-4.9069
0.2327
921
0.2327
921
X-RAY DIFFRACTION
100
4.9069-5.0821
0.2352
923
0.2352
923
X-RAY DIFFRACTION
100
5.0821-5.2854
0.2251
925
0.2251
925
X-RAY DIFFRACTION
100
5.2854-5.5256
0.2533
930
0.2533
930
X-RAY DIFFRACTION
100
5.5256-5.8165
0.2522
926
0.2522
926
X-RAY DIFFRACTION
100
5.8165-6.1802
0.2688
915
0.2688
915
X-RAY DIFFRACTION
100
6.1802-6.6563
0.2391
939
0.2391
939
X-RAY DIFFRACTION
100
6.6563-7.3242
0.2528
923
0.2528
923
X-RAY DIFFRACTION
100
7.3242-8.3794
0.1977
924
0.1977
924
X-RAY DIFFRACTION
100
8.3794-10.5395
0.1571
897
0.1571
897
X-RAY DIFFRACTION
98
10.5395-48.7647
0.2263
879
0.2263
879
X-RAY DIFFRACTION
94
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
2.6901
-1.9883
-0.8426
1.7598
0.7235
2.5264
-0.1708
0.6019
-0.754
-0.0284
-0.5682
0.9586
0.1295
-1.1041
-0.34
0.7764
-0.2381
0.3037
0.8239
-0.1982
1.1378
2.5847
65.618
220.2009
2
0.8211
0.7356
0.756
1.4418
-0.6949
3.149
-0.5446
0.3439
0.012
-0.7531
-0.1885
-0.8763
-0.1118
1.8975
-0.1382
0.6319
0.072
-0.0237
1.137
-0.0537
0.7479
21.9831
92.8907
211.9689
3
1.7258
0.1089
0.7908
2.1352
-0.0415
1.5943
0.0086
0.9739
-0.1905
-0.7719
-0.0572
0.1353
-0.089
0.0347
0.0286
0.7518
-0.0293
-0.0301
0.9239
-0.2016
0.4693
10.0269
88.9554
197.9496
4
2.3194
0.2988
-0.5933
1.6144
0.7232
2.3929
-0.7389
-0.2837
0.1716
-0.0115
-0.0258
0.351
0.1504
0.0278
-1.7612
0.7413
-0.081
-0.3693
0.7028
-0.25
0.7591
-23.5351
109.7471
196.224
5
4.9522
-1.131
4.4544
6.4105
-1.169
4.0065
0.2533
-1.6839
-0.047
1.6567
0.2773
0.8142
-0.178
-0.9915
0.5976
0.4269
-0.0335
0.1099
0.6344
-0.395
0.7228
-10.8946
113.9094
227.9439
6
1.0408
0.209
0.6832
1.3678
-0.7006
2.0867
-0.0221
-0.3341
0.1035
0.148
-0.2761
1.0571
-0.2578
-0.7249
-0.3084
0.4219
-0.1042
0.0902
0.6873
-0.1984
0.744
-19.3661
97.3094
226.5143
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAIN A AND RESID -1:209)
2
X-RAY DIFFRACTION
2
(CHAINAANDRESID210:253)
3
X-RAY DIFFRACTION
3
(CHAINAANDRESID254:438)
4
X-RAY DIFFRACTION
4
(CHAIN B AND RESID -1:209)
5
X-RAY DIFFRACTION
5
(CHAINBANDRESID210:253)
6
X-RAY DIFFRACTION
6
(CHAINBANDRESID254:438)
+
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