Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED ...Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED MUTATIONS WERE MADE USING PCR. Plasmid: PTRCHISB_DGKA_DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)
Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M): ALSO CONTAINS THE R-ISOMER OF THIS LIPID
Sequence details
THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE ...THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 19
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Sample preparation
Crystal
Density Matthews: 3.95 Å3/Da / Density % sol: 68.86 % / Description: NONE
Crystal grow
Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE CELSIUS WITH THE 7.8 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID.
Type: MARRESEARCH / Detector: CCD / Date: Jun 13, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS
Radiation
Monochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.0332
1
2
0.97944
1
Reflection
Resolution: 2.05→58.04 Å / Num. obs: 62716 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shell
Resolution: 2.05→2.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 99.5
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XSCALE
datascaling
SHELX
CDE
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.05→51.894 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM ...Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM SEMET DATA WERE USED, TARGET MLHL, UNTIL THE FINAL ROUNDS OF REFINEMENT WHERE TARGET WAS ML. THE FOLLOWING RESIDUES COULD NOT BE PLACED INTO ELECTRON DENSITY DUE TO DISORDER OR FLEXIBILITY - A1-5, B1-23, C1-31, D1-13, E1-35, E47-49, F1-33.
Rfactor
Num. reflection
% reflection
Rfree
0.2167
3161
5.1 %
Rwork
0.1959
-
-
obs
0.1969
62622
99.66 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 47.383 Å2
Refinement step
Cycle: LAST / Resolution: 2.05→51.894 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4416
0
306
187
4909
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
4932
X-RAY DIFFRACTION
f_angle_d
0.536
6687
X-RAY DIFFRACTION
f_dihedral_angle_d
14.95
1866
X-RAY DIFFRACTION
f_chiral_restr
0.039
836
X-RAY DIFFRACTION
f_plane_restr
0.002
797
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.05-2.0806
0.3286
138
0.2835
2567
X-RAY DIFFRACTION
99
2.0806-2.1131
0.2692
139
0.2669
2519
X-RAY DIFFRACTION
99
2.1131-2.1478
0.2747
170
0.2499
2525
X-RAY DIFFRACTION
100
2.1478-2.1848
0.2784
132
0.2258
2549
X-RAY DIFFRACTION
100
2.1848-2.2245
0.2651
120
0.2424
2557
X-RAY DIFFRACTION
100
2.2245-2.2673
0.3645
131
0.3305
2502
X-RAY DIFFRACTION
98
2.2673-2.3136
0.2687
145
0.2277
2548
X-RAY DIFFRACTION
99
2.3136-2.3639
0.222
154
0.1855
2551
X-RAY DIFFRACTION
100
2.3639-2.4189
0.1914
136
0.1659
2583
X-RAY DIFFRACTION
100
2.4189-2.4794
0.2136
116
0.1639
2566
X-RAY DIFFRACTION
100
2.4794-2.5464
0.2049
110
0.1691
2602
X-RAY DIFFRACTION
100
2.5464-2.6213
0.1756
141
0.1653
2564
X-RAY DIFFRACTION
100
2.6213-2.7059
0.1919
147
0.1621
2583
X-RAY DIFFRACTION
100
2.7059-2.8027
0.2015
129
0.1658
2560
X-RAY DIFFRACTION
100
2.8027-2.9149
0.1953
122
0.1734
2595
X-RAY DIFFRACTION
100
2.9149-3.0475
0.225
132
0.1717
2613
X-RAY DIFFRACTION
100
3.0475-3.2082
0.1993
151
0.1736
2573
X-RAY DIFFRACTION
100
3.2082-3.4091
0.2078
142
0.1813
2606
X-RAY DIFFRACTION
100
3.4091-3.6723
0.1874
144
0.1805
2601
X-RAY DIFFRACTION
100
3.6723-4.0417
0.198
145
0.178
2622
X-RAY DIFFRACTION
100
4.0417-4.6262
0.1765
141
0.1715
2645
X-RAY DIFFRACTION
100
4.6262-5.8273
0.2408
130
0.2239
2675
X-RAY DIFFRACTION
100
5.8273-51.9105
0.246
146
0.2332
2755
X-RAY DIFFRACTION
99
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
2.8943
-1.6045
1.5821
1.3769
-0.738
7.5994
-0.0831
-0.019
-0.5013
0.1429
0.0031
0.082
0.5592
0.0164
0.1008
0.2263
-0.0991
0.0267
0.273
0.01
0.3517
35.7316
61.1331
87.7602
2
3.1871
0.0658
0.1546
4.2991
2.3319
5.7789
-0.0204
0.0666
0.1041
-0.1568
-0.1616
0.1773
-0.6629
-0.1263
0.1862
0.1197
0.0122
-0.005
0.2018
0.0235
0.2074
43.0008
72.3539
81.8209
3
1.6603
-0.6219
-2.1373
2.4782
2.8098
3.5495
-0.1542
-0.1507
-0.2265
0.4605
0.2339
-0.1261
0.7491
0.5148
-0.0361
0.2324
0.0639
-0.0219
0.3281
-0.0084
0.3016
55.9198
57.8559
82.749
4
2.5588
0.0039
0.5844
2.794
0.3931
2.7023
0.0113
0.1955
-0.2064
0.2078
0.1019
0.0536
0.7328
-0.4637
-0.0041
0.1626
-0.0422
0.004
0.1848
0.0244
0.2644
44.4662
58.1164
85.2764
5
1.0808
1.277
-0.3757
6.6828
3.3318
5.5479
0.3714
-0.1332
1.134
-0.6634
-0.6503
0.0715
-0.3924
-0.0964
0.2714
0.3407
0.0642
0.1272
0.4156
0.0158
0.5819
55.4172
77.7796
67.5259
6
2.2427
-0.7066
-2.3414
1.9581
0.2992
3.2034
0.091
-0.3301
0.1053
0.2934
0.117
-0.1954
-0.2743
0.5533
-0.1931
0.15
-0.0459
-0.0202
0.3054
-0.0224
0.2543
58.129
70.373
83.8236
7
1.6336
-0.25
-1.2137
3.8337
-0.3952
2.974
-0.0603
-0.0384
0.0262
0.1389
0.0629
-0.1231
0.139
0.1599
-0.0118
0.1668
0.0201
-0.0155
0.211
-0.0344
0.2342
71.6347
50.0338
62.807
8
3.4837
-0.5308
-1.3071
4.1265
2.4377
8.8106
-0.1211
0.2639
-0.1867
0.0758
-0.251
0.4164
0.35
-0.789
0.3016
0.224
0.0058
0.0208
0.2208
-0.0256
0.3731
62.1793
42.3171
60.2712
9
3.2865
0.8288
-1.5619
3.2181
1.968
2.0614
0.0351
-0.0177
-0.3406
0.1526
0.1648
-0.3227
0.2461
1.0095
-0.1275
0.2368
0.1395
-0.0061
0.3383
-0.0737
0.3771
80.4984
39.114
59.5171
10
4.432
-0.5471
-0.8099
6.8295
-6.0189
5.6832
0.4021
-0.3458
0.2273
1.1071
0.3199
-0.8379
-0.3943
2.811
0.4188
1.1816
-0.0563
-0.0745
2.1323
-0.0444
0.1888
86.4798
44.2892
83.9134
11
9.052
3.6042
-2.6814
7.8913
-1.7406
7.2895
0.1587
0.2987
-0.8865
0.3492
0.1401
-0.1381
0.5938
-0.1999
-0.2919
1.2071
-0.2527
0.026
0.6322
-0.0767
1.6676
57.9186
26.4447
61.9196
12
1.8825
-0.3492
0.2257
2.4074
1.3988
3.5693
-0.1053
-0.2459
-0.2694
0.6037
0.0158
0.1946
2.0097
-0.3692
-0.044
0.6687
-0.0288
0.027
0.2098
0.0034
0.3139
68.9322
30.4231
61.8974
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINAANDRESID6:47)
2
X-RAY DIFFRACTION
2
(CHAINAANDRESID48:121)
3
X-RAY DIFFRACTION
3
(CHAINBANDRESID24:83)
4
X-RAY DIFFRACTION
4
(CHAINBANDRESID84:121)
5
X-RAY DIFFRACTION
5
(CHAINCANDRESID32:57)
6
X-RAY DIFFRACTION
6
(CHAINCANDRESID58:121)
7
X-RAY DIFFRACTION
7
(CHAINDANDRESID14:80)
8
X-RAY DIFFRACTION
8
(CHAINDANDRESID81:121)
9
X-RAY DIFFRACTION
9
(CHAINEANDRESID36:116)
10
X-RAY DIFFRACTION
10
(CHAINEANDRESID117:121)
11
X-RAY DIFFRACTION
11
(CHAINFANDRESID29:37)
12
X-RAY DIFFRACTION
12
(CHAINFANDRESID38:121)
+
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