0.016601
0.000000
0.000000
0.000000
0.016601
0.000000
0.000000
0.000000
0.005839
0.00000
0.00000
0.00000
Arai, R.
Nishino, A.
Nagano, K.
Kamo-Uchikubo, T.
Nishimoto, M.
Toyama, M.
Terada, T.
Murayama, K.
Shirouzu, M.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
60.236
60.236
171.276
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H11 N O3 S2
197.276
n
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
K 1
39.098
POTASSIUM ION
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C4 H6 O6
150.087
L(+)-TARTARIC ACID
non-polymer
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
C20 H42 O11
458.541
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
DECAETHYLENE GLYCOL
non-polymer
US
J.Struct.Biol.
JSBIEM
0803
1047-8477
168
575
581
10.1016/j.jsb.2009.07.007
19602440
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
2009
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
100
1
1
Two dimensional focusing mirror
CCD
2005-04-16
RIGAKU JUPITER 210
Two dimensional focusing mirror
CCD
2005-05-25
RIGAKU JUPITER 210
Si double crystal
SINGLE WAVELENGTH
M
x-ray
1
Si double crystal
MAD
M
x-ray
1
1.00000
1.0
1.07181
1.0
1.07216
1.0
1.05000
1.0
BL26B1
SPring-8
1.00000
SYNCHROTRON
SPRING-8 BEAMLINE BL26B1
BL26B1
SPring-8
1.07181, 1.07216, 1.05000
SYNCHROTRON
SPRING-8 BEAMLINE BL26B1
30144.529
hypothetical protein TTHA1568
1
man
polymer
39.098
POTASSIUM ION
1
syn
non-polymer
150.087
L(+)-TARTARIC ACID
1
syn
non-polymer
458.541
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
1
syn
non-polymer
18.015
water
316
nat
water
no
yes
MEALRLGFSP(CME)PNDTFIFYALVHGRVESPVPLEPVLEDVETLNRWALEGRLPLTKLSYAAYAQVRDRYVALRSGGA
LGRGVGPLVVARGPLQALEGLRVAVPGRHTTAYFLLSLYAQGFVPVEVRYDRILPMVAQGEVEAGLIIHESRFTYPRYGL
VQVVDLGAWWEERTGLPLPLGAILARRDLGEGLIRALDEAVRRSVAYALAHPEEALDYMRAHAQELSDEVIWAHVHTYVN
AFSLDVGEEGERAVARLFAEAEARGLAAPSPRPLFV
MEALRLGFSPCPNDTFIFYALVHGRVESPVPLEPVLEDVETLNRWALEGRLPLTKLSYAAYAQVRDRYVALRSGGALGRG
VGPLVVARGPLQALEGLRVAVPGRHTTAYFLLSLYAQGFVPVEVRYDRILPMVAQGEVEAGLIIHESRFTYPRYGLVQVV
DLGAWWEERTGLPLPLGAILARRDLGEGLIRALDEAVRRSVAYALAHPEEALDYMRAHAQELSDEVIWAHVHTYVNAFSL
DVGEEGERAVARLFAEAEARGLAAPSPRPLFV
A
ttk003001639.1
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Thermus
Thermus thermophilus
HB8
Escherichia
Escherichia coli
sample
TTHA1568
300852
Thermus thermophilus
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
pET11
2
2.64
53.3
VAPOR DIFFUSION, HANGING DROP
7.5
0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 2.5% PEG 5000, MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
VAPOR DIFFUSION, HANGING DROP
8.0
0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 0.75% PEG 5000, MME, 5mM K2PtCl4, 16h soaking, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
1
0
2006-01-13
1
1
2008-04-30
1
2
2011-07-13
STRUCTURE OF THE SAME PROTEIN WITHOUT MODIFICATION AT CYS11
Y
PDBJ
Y
PDBJ
2005-07-13
REL
REL
K
POTASSIUM ION
TLA
L(+)-TARTARIC ACID
XPE
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
HOH
water
K
601
2
K
K
601
A
TLA
401
3
TLA
TLA
401
A
XPE
501
4
XPE
XPE
501
A
HOH
1
5
HOH
HOH
602
A
HOH
2
5
HOH
HOH
603
A
HOH
3
5
HOH
HOH
604
A
HOH
4
5
HOH
HOH
605
A
HOH
5
5
HOH
HOH
606
A
HOH
6
5
HOH
HOH
607
A
HOH
7
5
HOH
HOH
608
A
HOH
8
5
HOH
HOH
609
A
HOH
9
5
HOH
HOH
610
A
HOH
10
5
HOH
HOH
611
A
HOH
11
5
HOH
HOH
612
A
HOH
12
5
HOH
HOH
613
A
HOH
13
5
HOH
HOH
614
A
HOH
14
5
HOH
HOH
615
A
HOH
15
5
HOH
HOH
616
A
HOH
16
5
HOH
HOH
617
A
HOH
17
5
HOH
HOH
618
A
HOH
18
5
HOH
HOH
619
A
HOH
19
5
HOH
HOH
620
A
HOH
20
5
HOH
HOH
621
A
HOH
21
5
HOH
HOH
622
A
HOH
22
5
HOH
HOH
623
A
HOH
23
5
HOH
HOH
624
A
HOH
24
5
HOH
HOH
625
A
HOH
25
5
HOH
HOH
626
A
HOH
26
5
HOH
HOH
627
A
HOH
27
5
HOH
HOH
628
A
HOH
28
5
HOH
HOH
629
A
HOH
29
5
HOH
HOH
630
A
HOH
30
5
HOH
HOH
631
A
HOH
31
5
HOH
HOH
632
A
HOH
32
5
HOH
HOH
633
A
HOH
33
5
HOH
HOH
634
A
HOH
34
5
HOH
HOH
635
A
HOH
35
5
HOH
HOH
636
A
HOH
36
5
HOH
HOH
637
A
HOH
37
5
HOH
HOH
638
A
HOH
38
5
HOH
HOH
639
A
HOH
39
5
HOH
HOH
640
A
HOH
40
5
HOH
HOH
641
A
HOH
41
5
HOH
HOH
642
A
HOH
42
5
HOH
HOH
643
A
HOH
43
5
HOH
HOH
644
A
HOH
44
5
HOH
HOH
645
A
HOH
45
5
HOH
HOH
646
A
HOH
46
5
HOH
HOH
647
A
HOH
47
5
HOH
HOH
648
A
HOH
48
5
HOH
HOH
649
A
HOH
49
5
HOH
HOH
650
A
HOH
50
5
HOH
HOH
651
A
HOH
51
5
HOH
HOH
652
A
HOH
52
5
HOH
HOH
653
A
HOH
53
5
HOH
HOH
654
A
HOH
54
5
HOH
HOH
655
A
HOH
55
5
HOH
HOH
656
A
HOH
56
5
HOH
HOH
657
A
HOH
57
5
HOH
HOH
658
A
HOH
58
5
HOH
HOH
659
A
HOH
59
5
HOH
HOH
660
A
HOH
60
5
HOH
HOH
661
A
HOH
61
5
HOH
HOH
662
A
HOH
62
5
HOH
HOH
663
A
HOH
63
5
HOH
HOH
664
A
HOH
64
5
HOH
HOH
665
A
HOH
65
5
HOH
HOH
666
A
HOH
66
5
HOH
HOH
667
A
HOH
67
5
HOH
HOH
668
A
HOH
68
5
HOH
HOH
669
A
HOH
69
5
HOH
HOH
670
A
HOH
70
5
HOH
HOH
671
A
HOH
71
5
HOH
HOH
672
A
HOH
72
5
HOH
HOH
673
A
HOH
73
5
HOH
HOH
674
A
HOH
74
5
HOH
HOH
675
A
HOH
75
5
HOH
HOH
676
A
HOH
76
5
HOH
HOH
677
A
HOH
77
5
HOH
HOH
678
A
HOH
78
5
HOH
HOH
679
A
HOH
79
5
HOH
HOH
680
A
HOH
80
5
HOH
HOH
681
A
HOH
81
5
HOH
HOH
682
A
HOH
82
5
HOH
HOH
683
A
HOH
83
5
HOH
HOH
684
A
HOH
84
5
HOH
HOH
685
A
HOH
85
5
HOH
HOH
686
A
HOH
86
5
HOH
HOH
687
A
HOH
87
5
HOH
HOH
688
A
HOH
88
5
HOH
HOH
689
A
HOH
89
5
HOH
HOH
690
A
HOH
90
5
HOH
HOH
691
A
HOH
91
5
HOH
HOH
692
A
HOH
92
5
HOH
HOH
693
A
HOH
93
5
HOH
HOH
694
A
HOH
94
5
HOH
HOH
695
A
HOH
95
5
HOH
HOH
696
A
HOH
96
5
HOH
HOH
697
A
HOH
97
5
HOH
HOH
698
A
HOH
98
5
HOH
HOH
699
A
HOH
99
5
HOH
HOH
700
A
HOH
100
5
HOH
HOH
701
A
HOH
101
5
HOH
HOH
702
A
HOH
102
5
HOH
HOH
703
A
HOH
103
5
HOH
HOH
704
A
HOH
104
5
HOH
HOH
705
A
HOH
105
5
HOH
HOH
706
A
HOH
106
5
HOH
HOH
707
A
HOH
107
5
HOH
HOH
708
A
HOH
108
5
HOH
HOH
709
A
HOH
109
5
HOH
HOH
710
A
HOH
110
5
HOH
HOH
711
A
HOH
111
5
HOH
HOH
712
A
HOH
112
5
HOH
HOH
713
A
HOH
113
5
HOH
HOH
714
A
HOH
114
5
HOH
HOH
715
A
HOH
115
5
HOH
HOH
716
A
HOH
116
5
HOH
HOH
717
A
HOH
117
5
HOH
HOH
718
A
HOH
118
5
HOH
HOH
719
A
HOH
119
5
HOH
HOH
720
A
HOH
120
5
HOH
HOH
721
A
HOH
121
5
HOH
HOH
722
A
HOH
122
5
HOH
HOH
723
A
HOH
123
5
HOH
HOH
724
A
HOH
124
5
HOH
HOH
725
A
HOH
125
5
HOH
HOH
726
A
HOH
126
5
HOH
HOH
727
A
HOH
127
5
HOH
HOH
728
A
HOH
128
5
HOH
HOH
729
A
HOH
129
5
HOH
HOH
730
A
HOH
130
5
HOH
HOH
731
A
HOH
131
5
HOH
HOH
732
A
HOH
132
5
HOH
HOH
733
A
HOH
133
5
HOH
HOH
734
A
HOH
134
5
HOH
HOH
735
A
HOH
135
5
HOH
HOH
736
A
HOH
136
5
HOH
HOH
737
A
HOH
137
5
HOH
HOH
738
A
HOH
138
5
HOH
HOH
739
A
HOH
139
5
HOH
HOH
740
A
HOH
140
5
HOH
HOH
741
A
HOH
141
5
HOH
HOH
742
A
HOH
142
5
HOH
HOH
743
A
HOH
143
5
HOH
HOH
744
A
HOH
144
5
HOH
HOH
745
A
HOH
145
5
HOH
HOH
746
A
HOH
146
5
HOH
HOH
747
A
HOH
147
5
HOH
HOH
748
A
HOH
148
5
HOH
HOH
749
A
HOH
149
5
HOH
HOH
750
A
HOH
150
5
HOH
HOH
751
A
HOH
151
5
HOH
HOH
752
A
HOH
152
5
HOH
HOH
753
A
HOH
153
5
HOH
HOH
754
A
HOH
154
5
HOH
HOH
755
A
HOH
155
5
HOH
HOH
756
A
HOH
156
5
HOH
HOH
757
A
HOH
157
5
HOH
HOH
758
A
HOH
158
5
HOH
HOH
759
A
HOH
159
5
HOH
HOH
760
A
HOH
160
5
HOH
HOH
761
A
HOH
161
5
HOH
HOH
762
A
HOH
162
5
HOH
HOH
763
A
HOH
163
5
HOH
HOH
764
A
HOH
164
5
HOH
HOH
765
A
HOH
165
5
HOH
HOH
766
A
HOH
166
5
HOH
HOH
767
A
HOH
167
5
HOH
HOH
768
A
HOH
168
5
HOH
HOH
769
A
HOH
169
5
HOH
HOH
770
A
HOH
170
5
HOH
HOH
771
A
HOH
171
5
HOH
HOH
772
A
HOH
172
5
HOH
HOH
773
A
HOH
173
5
HOH
HOH
774
A
HOH
174
5
HOH
HOH
775
A
HOH
175
5
HOH
HOH
776
A
HOH
176
5
HOH
HOH
777
A
HOH
177
5
HOH
HOH
778
A
HOH
178
5
HOH
HOH
779
A
HOH
179
5
HOH
HOH
780
A
HOH
180
5
HOH
HOH
781
A
HOH
181
5
HOH
HOH
782
A
HOH
182
5
HOH
HOH
783
A
HOH
183
5
HOH
HOH
784
A
HOH
184
5
HOH
HOH
785
A
HOH
185
5
HOH
HOH
786
A
HOH
186
5
HOH
HOH
787
A
HOH
187
5
HOH
HOH
788
A
HOH
188
5
HOH
HOH
789
A
HOH
189
5
HOH
HOH
790
A
HOH
190
5
HOH
HOH
791
A
HOH
191
5
HOH
HOH
792
A
HOH
192
5
HOH
HOH
793
A
HOH
193
5
HOH
HOH
794
A
HOH
194
5
HOH
HOH
795
A
HOH
195
5
HOH
HOH
796
A
HOH
196
5
HOH
HOH
797
A
HOH
197
5
HOH
HOH
798
A
HOH
198
5
HOH
HOH
799
A
HOH
199
5
HOH
HOH
800
A
HOH
200
5
HOH
HOH
801
A
HOH
201
5
HOH
HOH
802
A
HOH
202
5
HOH
HOH
803
A
HOH
203
5
HOH
HOH
804
A
HOH
204
5
HOH
HOH
805
A
HOH
205
5
HOH
HOH
806
A
HOH
206
5
HOH
HOH
807
A
HOH
207
5
HOH
HOH
808
A
HOH
208
5
HOH
HOH
809
A
HOH
209
5
HOH
HOH
810
A
HOH
210
5
HOH
HOH
811
A
HOH
211
5
HOH
HOH
812
A
HOH
212
5
HOH
HOH
813
A
HOH
213
5
HOH
HOH
814
A
HOH
214
5
HOH
HOH
815
A
HOH
215
5
HOH
HOH
816
A
HOH
216
5
HOH
HOH
817
A
HOH
217
5
HOH
HOH
818
A
HOH
218
5
HOH
HOH
819
A
HOH
219
5
HOH
HOH
820
A
HOH
220
5
HOH
HOH
821
A
HOH
221
5
HOH
HOH
822
A
HOH
222
5
HOH
HOH
823
A
HOH
223
5
HOH
HOH
824
A
HOH
224
5
HOH
HOH
825
A
HOH
225
5
HOH
HOH
826
A
HOH
226
5
HOH
HOH
827
A
HOH
227
5
HOH
HOH
828
A
HOH
228
5
HOH
HOH
829
A
HOH
229
5
HOH
HOH
830
A
HOH
230
5
HOH
HOH
831
A
HOH
231
5
HOH
HOH
832
A
HOH
232
5
HOH
HOH
833
A
HOH
233
5
HOH
HOH
834
A
HOH
234
5
HOH
HOH
835
A
HOH
235
5
HOH
HOH
836
A
HOH
236
5
HOH
HOH
837
A
HOH
237
5
HOH
HOH
838
A
HOH
238
5
HOH
HOH
839
A
HOH
239
5
HOH
HOH
840
A
HOH
240
5
HOH
HOH
841
A
HOH
241
5
HOH
HOH
842
A
HOH
242
5
HOH
HOH
843
A
HOH
243
5
HOH
HOH
844
A
HOH
244
5
HOH
HOH
845
A
HOH
245
5
HOH
HOH
846
A
HOH
246
5
HOH
HOH
847
A
HOH
247
5
HOH
HOH
848
A
HOH
248
5
HOH
HOH
849
A
HOH
249
5
HOH
HOH
850
A
HOH
250
5
HOH
HOH
851
A
HOH
251
5
HOH
HOH
852
A
HOH
252
5
HOH
HOH
853
A
HOH
253
5
HOH
HOH
854
A
HOH
254
5
HOH
HOH
855
A
HOH
255
5
HOH
HOH
856
A
HOH
256
5
HOH
HOH
857
A
HOH
257
5
HOH
HOH
858
A
HOH
258
5
HOH
HOH
859
A
HOH
259
5
HOH
HOH
860
A
HOH
260
5
HOH
HOH
861
A
HOH
261
5
HOH
HOH
862
A
HOH
262
5
HOH
HOH
863
A
HOH
263
5
HOH
HOH
864
A
HOH
264
5
HOH
HOH
865
A
HOH
265
5
HOH
HOH
866
A
HOH
266
5
HOH
HOH
867
A
HOH
267
5
HOH
HOH
868
A
HOH
268
5
HOH
HOH
869
A
HOH
269
5
HOH
HOH
870
A
HOH
270
5
HOH
HOH
871
A
HOH
271
5
HOH
HOH
872
A
HOH
272
5
HOH
HOH
873
A
HOH
273
5
HOH
HOH
874
A
HOH
274
5
HOH
HOH
875
A
HOH
275
5
HOH
HOH
876
A
HOH
276
5
HOH
HOH
877
A
HOH
277
5
HOH
HOH
878
A
HOH
278
5
HOH
HOH
879
A
HOH
279
5
HOH
HOH
880
A
HOH
280
5
HOH
HOH
881
A
HOH
281
5
HOH
HOH
882
A
HOH
282
5
HOH
HOH
883
A
HOH
283
5
HOH
HOH
884
A
HOH
284
5
HOH
HOH
885
A
HOH
285
5
HOH
HOH
886
A
HOH
286
5
HOH
HOH
887
A
HOH
287
5
HOH
HOH
888
A
HOH
288
5
HOH
HOH
889
A
HOH
289
5
HOH
HOH
890
A
HOH
290
5
HOH
HOH
891
A
HOH
291
5
HOH
HOH
892
A
HOH
292
5
HOH
HOH
893
A
HOH
293
5
HOH
HOH
894
A
HOH
294
5
HOH
HOH
895
A
HOH
295
5
HOH
HOH
896
A
HOH
296
5
HOH
HOH
897
A
HOH
297
5
HOH
HOH
898
A
HOH
298
5
HOH
HOH
899
A
HOH
299
5
HOH
HOH
900
A
HOH
300
5
HOH
HOH
901
A
HOH
301
5
HOH
HOH
902
A
HOH
302
5
HOH
HOH
903
A
HOH
303
5
HOH
HOH
904
A
HOH
304
5
HOH
HOH
905
A
HOH
305
5
HOH
HOH
906
A
HOH
306
5
HOH
HOH
907
A
HOH
307
5
HOH
HOH
908
A
HOH
308
5
HOH
HOH
909
A
HOH
309
5
HOH
HOH
910
A
HOH
310
5
HOH
HOH
911
A
HOH
311
5
HOH
HOH
912
A
HOH
312
5
HOH
HOH
913
A
HOH
313
5
HOH
HOH
914
A
HOH
314
5
HOH
HOH
915
A
HOH
315
5
HOH
HOH
916
A
HOH
316
5
HOH
HOH
917
A
n
1
1
A
n
2
2
A
ALA
3
n
3
ALA
3
A
LEU
4
n
4
LEU
4
A
ARG
5
n
5
ARG
5
A
LEU
6
n
6
LEU
6
A
GLY
7
n
7
GLY
7
A
PHE
8
n
8
PHE
8
A
SER
9
n
9
SER
9
A
PRO
10
n
10
PRO
10
A
CME
11
n
11
CME
11
A
PRO
12
n
12
PRO
12
A
ASN
13
n
13
ASN
13
A
ASP
14
n
14
ASP
14
A
THR
15
n
15
THR
15
A
PHE
16
n
16
PHE
16
A
ILE
17
n
17
ILE
17
A
PHE
18
n
18
PHE
18
A
TYR
19
n
19
TYR
19
A
ALA
20
n
20
ALA
20
A
LEU
21
n
21
LEU
21
A
VAL
22
n
22
VAL
22
A
HIS
23
n
23
HIS
23
A
GLY
24
n
24
GLY
24
A
ARG
25
n
25
ARG
25
A
VAL
26
n
26
VAL
26
A
GLU
27
n
27
GLU
27
A
SER
28
n
28
SER
28
A
PRO
29
n
29
PRO
29
A
VAL
30
n
30
VAL
30
A
PRO
31
n
31
PRO
31
A
LEU
32
n
32
LEU
32
A
GLU
33
n
33
GLU
33
A
PRO
34
n
34
PRO
34
A
VAL
35
n
35
VAL
35
A
LEU
36
n
36
LEU
36
A
GLU
37
n
37
GLU
37
A
ASP
38
n
38
ASP
38
A
VAL
39
n
39
VAL
39
A
GLU
40
n
40
GLU
40
A
THR
41
n
41
THR
41
A
LEU
42
n
42
LEU
42
A
ASN
43
n
43
ASN
43
A
ARG
44
n
44
ARG
44
A
TRP
45
n
45
TRP
45
A
ALA
46
n
46
ALA
46
A
LEU
47
n
47
LEU
47
A
GLU
48
n
48
GLU
48
A
GLY
49
n
49
GLY
49
A
ARG
50
n
50
ARG
50
A
LEU
51
n
51
LEU
51
A
PRO
52
n
52
PRO
52
A
LEU
53
n
53
LEU
53
A
THR
54
n
54
THR
54
A
LYS
55
n
55
LYS
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
TYR
58
n
58
TYR
58
A
ALA
59
n
59
ALA
59
A
ALA
60
n
60
ALA
60
A
TYR
61
n
61
TYR
61
A
ALA
62
n
62
ALA
62
A
GLN
63
n
63
GLN
63
A
VAL
64
n
64
VAL
64
A
ARG
65
n
65
ARG
65
A
ASP
66
n
66
ASP
66
A
ARG
67
n
67
ARG
67
A
TYR
68
n
68
TYR
68
A
VAL
69
n
69
VAL
69
A
ALA
70
n
70
ALA
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
SER
73
n
73
SER
73
A
GLY
74
n
74
GLY
74
A
GLY
75
n
75
GLY
75
A
ALA
76
n
76
ALA
76
A
LEU
77
n
77
LEU
77
A
GLY
78
n
78
GLY
78
A
ARG
79
n
79
ARG
79
A
GLY
80
n
80
GLY
80
A
VAL
81
n
81
VAL
81
A
GLY
82
n
82
GLY
82
A
PRO
83
n
83
PRO
83
A
LEU
84
n
84
LEU
84
A
VAL
85
n
85
VAL
85
A
VAL
86
n
86
VAL
86
A
ALA
87
n
87
ALA
87
A
ARG
88
n
88
ARG
88
A
GLY
89
n
89
GLY
89
A
PRO
90
n
90
PRO
90
A
LEU
91
n
91
LEU
91
A
GLN
92
n
92
GLN
92
A
ALA
93
n
93
ALA
93
A
LEU
94
n
94
LEU
94
A
GLU
95
n
95
GLU
95
A
GLY
96
n
96
GLY
96
A
LEU
97
n
97
LEU
97
A
ARG
98
n
98
ARG
98
A
VAL
99
n
99
VAL
99
A
ALA
100
n
100
ALA
100
A
VAL
101
n
101
VAL
101
A
PRO
102
n
102
PRO
102
A
GLY
103
n
103
GLY
103
A
ARG
104
n
104
ARG
104
A
HIS
105
n
105
HIS
105
A
THR
106
n
106
THR
106
A
THR
107
n
107
THR
107
A
ALA
108
n
108
ALA
108
A
TYR
109
n
109
TYR
109
A
PHE
110
n
110
PHE
110
A
LEU
111
n
111
LEU
111
A
LEU
112
n
112
LEU
112
A
SER
113
n
113
SER
113
A
LEU
114
n
114
LEU
114
A
TYR
115
n
115
TYR
115
A
ALA
116
n
116
ALA
116
A
GLN
117
n
117
GLN
117
A
GLY
118
n
118
GLY
118
A
PHE
119
n
119
PHE
119
A
VAL
120
n
120
VAL
120
A
PRO
121
n
121
PRO
121
A
VAL
122
n
122
VAL
122
A
GLU
123
n
123
GLU
123
A
VAL
124
n
124
VAL
124
A
ARG
125
n
125
ARG
125
A
TYR
126
n
126
TYR
126
A
ASP
127
n
127
ASP
127
A
ARG
128
n
128
ARG
128
A
ILE
129
n
129
ILE
129
A
LEU
130
n
130
LEU
130
A
PRO
131
n
131
PRO
131
A
MET
132
n
132
MET
132
A
VAL
133
n
133
VAL
133
A
ALA
134
n
134
ALA
134
A
GLN
135
n
135
GLN
135
A
GLY
136
n
136
GLY
136
A
GLU
137
n
137
GLU
137
A
VAL
138
n
138
VAL
138
A
GLU
139
n
139
GLU
139
A
ALA
140
n
140
ALA
140
A
GLY
141
n
141
GLY
141
A
LEU
142
n
142
LEU
142
A
ILE
143
n
143
ILE
143
A
ILE
144
n
144
ILE
144
A
HIS
145
n
145
HIS
145
A
GLU
146
n
146
GLU
146
A
SER
147
n
147
SER
147
A
ARG
148
n
148
ARG
148
A
PHE
149
n
149
PHE
149
A
THR
150
n
150
THR
150
A
TYR
151
n
151
TYR
151
A
PRO
152
n
152
PRO
152
A
ARG
153
n
153
ARG
153
A
TYR
154
n
154
TYR
154
A
GLY
155
n
155
GLY
155
A
LEU
156
n
156
LEU
156
A
VAL
157
n
157
VAL
157
A
GLN
158
n
158
GLN
158
A
VAL
159
n
159
VAL
159
A
VAL
160
n
160
VAL
160
A
ASP
161
n
161
ASP
161
A
LEU
162
n
162
LEU
162
A
GLY
163
n
163
GLY
163
A
ALA
164
n
164
ALA
164
A
TRP
165
n
165
TRP
165
A
TRP
166
n
166
TRP
166
A
GLU
167
n
167
GLU
167
A
GLU
168
n
168
GLU
168
A
ARG
169
n
169
ARG
169
A
THR
170
n
170
THR
170
A
GLY
171
n
171
GLY
171
A
LEU
172
n
172
LEU
172
A
PRO
173
n
173
PRO
173
A
LEU
174
n
174
LEU
174
A
PRO
175
n
175
PRO
175
A
LEU
176
n
176
LEU
176
A
GLY
177
n
177
GLY
177
A
ALA
178
n
178
ALA
178
A
ILE
179
n
179
ILE
179
A
LEU
180
n
180
LEU
180
A
ALA
181
n
181
ALA
181
A
ARG
182
n
182
ARG
182
A
ARG
183
n
183
ARG
183
A
ASP
184
n
184
ASP
184
A
LEU
185
n
185
LEU
185
A
GLY
186
n
186
GLY
186
A
GLU
187
n
187
GLU
187
A
GLY
188
n
188
GLY
188
A
LEU
189
n
189
LEU
189
A
ILE
190
n
190
ILE
190
A
ARG
191
n
191
ARG
191
A
ALA
192
n
192
ALA
192
A
LEU
193
n
193
LEU
193
A
ASP
194
n
194
ASP
194
A
GLU
195
n
195
GLU
195
A
ALA
196
n
196
ALA
196
A
VAL
197
n
197
VAL
197
A
ARG
198
n
198
ARG
198
A
ARG
199
n
199
ARG
199
A
SER
200
n
200
SER
200
A
VAL
201
n
201
VAL
201
A
ALA
202
n
202
ALA
202
A
TYR
203
n
203
TYR
203
A
ALA
204
n
204
ALA
204
A
LEU
205
n
205
LEU
205
A
ALA
206
n
206
ALA
206
A
HIS
207
n
207
HIS
207
A
PRO
208
n
208
PRO
208
A
GLU
209
n
209
GLU
209
A
GLU
210
n
210
GLU
210
A
ALA
211
n
211
ALA
211
A
LEU
212
n
212
LEU
212
A
ASP
213
n
213
ASP
213
A
TYR
214
n
214
TYR
214
A
MET
215
n
215
MET
215
A
ARG
216
n
216
ARG
216
A
ALA
217
n
217
ALA
217
A
HIS
218
n
218
HIS
218
A
ALA
219
n
219
ALA
219
A
GLN
220
n
220
GLN
220
A
GLU
221
n
221
GLU
221
A
LEU
222
n
222
LEU
222
A
SER
223
n
223
SER
223
A
ASP
224
n
224
ASP
224
A
GLU
225
n
225
GLU
225
A
VAL
226
n
226
VAL
226
A
ILE
227
n
227
ILE
227
A
TRP
228
n
228
TRP
228
A
ALA
229
n
229
ALA
229
A
HIS
230
n
230
HIS
230
A
VAL
231
n
231
VAL
231
A
HIS
232
n
232
HIS
232
A
THR
233
n
233
THR
233
A
TYR
234
n
234
TYR
234
A
VAL
235
n
235
VAL
235
A
ASN
236
n
236
ASN
236
A
ALA
237
n
237
ALA
237
A
PHE
238
n
238
PHE
238
A
SER
239
n
239
SER
239
A
LEU
240
n
240
LEU
240
A
ASP
241
n
241
ASP
241
A
VAL
242
n
242
VAL
242
A
GLY
243
n
243
GLY
243
A
GLU
244
n
244
GLU
244
A
GLU
245
n
245
GLU
245
A
GLY
246
n
246
GLY
246
A
GLU
247
n
247
GLU
247
A
ARG
248
n
248
ARG
248
A
ALA
249
n
249
ALA
249
A
VAL
250
n
250
VAL
250
A
ALA
251
n
251
ALA
251
A
ARG
252
n
252
ARG
252
A
LEU
253
n
253
LEU
253
A
PHE
254
n
254
PHE
254
A
ALA
255
n
255
ALA
255
A
GLU
256
n
256
GLU
256
A
ALA
257
n
257
ALA
257
A
GLU
258
n
258
GLU
258
A
ALA
259
n
259
ALA
259
A
ARG
260
n
260
ARG
260
A
GLY
261
n
261
GLY
261
A
LEU
262
n
262
LEU
262
A
ALA
263
n
263
ALA
263
A
ALA
264
n
264
ALA
264
A
PRO
265
n
265
PRO
265
A
SER
266
n
266
SER
266
A
PRO
267
n
267
PRO
267
A
ARG
268
n
268
ARG
268
A
PRO
269
n
269
PRO
269
A
LEU
270
n
270
LEU
270
A
PHE
271
n
271
PHE
271
A
VAL
272
n
272
VAL
272
A
author_defined_assembly
1
monomeric
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
PHE
149
A
O
PHE
149
1_555
82.4
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O4
XPE
1_555
125.0
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O4
XPE
1_555
145.3
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O19
XPE
1_555
112.2
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O19
XPE
1_555
104.9
A
XPE
501
D
O4
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O19
XPE
1_555
85.3
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O22
XPE
1_555
156.7
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O22
XPE
1_555
79.4
A
XPE
501
D
O4
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O22
XPE
1_555
77.7
A
XPE
501
D
O19
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O22
XPE
1_555
59.6
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
58.6
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
74.8
A
XPE
501
D
O4
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
100.2
A
XPE
501
D
O19
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
170.8
A
XPE
501
D
O22
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
128.6
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
57.4
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
116.6
A
XPE
501
D
O4
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
97.4
A
XPE
501
D
O19
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
60.0
A
XPE
501
D
O22
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
119.6
A
XPE
501
D
O10
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
111.7
A
XPE
501
D
O13
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
118.1
A
PHE
149
A
O
PHE
149
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
88.9
A
XPE
501
D
O4
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
60.5
A
XPE
501
D
O19
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
129.1
A
XPE
501
D
O22
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
76.0
A
XPE
501
D
O10
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
60.0
A
XPE
501
D
O16
XPE
1_555
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
151.2
A
CME
11
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
A
CME
11
CYS
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
GLU
33
A
O
GLU
33
A
N
LEU
4
A
N
LEU
4
A
N
GLY
7
A
N
GLY
7
A
O
LYS
55
A
O
LYS
55
A
N
THR
54
A
N
THR
54
A
O
LEU
180
A
O
LEU
180
A
O
ALA
181
A
O
ALA
181
A
N
VAL
69
A
N
VAL
69
A
O
GLU
33
A
O
GLU
33
A
N
LEU
4
A
N
LEU
4
A
N
GLY
7
A
N
GLY
7
A
O
LYS
55
A
O
LYS
55
A
N
THR
54
A
N
THR
54
A
O
LEU
180
A
O
LEU
180
A
O
GLY
177
A
O
GLY
177
A
N
ALA
76
A
N
ALA
76
A
O
VAL
122
A
O
VAL
122
A
N
VAL
101
A
N
VAL
101
A
N
ALA
100
A
N
ALA
100
A
O
LEU
142
A
O
LEU
142
A
O
ILE
143
A
O
ILE
143
A
N
LEU
84
A
N
LEU
84
A
N
VAL
85
A
N
VAL
85
A
O
VAL
159
A
O
VAL
159
1
A
HOH
905
E
HOH
1
A
MET
1
A
MET
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
A
O
O
HOH
HOH
713
897
1.97
1
A
A
OE2
NE
GLU
ARG
244
248
2.19
1
A
HIS
145
54.61
-135.15
protein_rep_CME.param
protein_CME.top
water_rep.param
water.top
ion.param
ion.top
tla.param
tla.top
pegf_7.param
pegf_7.top
20.7
-0.16
0.00
0.00
-0.16
0.00
0.32
0.209
0.003
0.182
1.55
42.82
4520
44576
10.1
95.1
RANDOM
670101.11
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MAD
MAXIMUM LIKELIHOOD
FLAT MODEL
49.8724
0.368804
0.19
0.16
5.00
0.12
0.09
1.55
42.82
316
2471
42
0
2113
0.010
1.6
22.5
1.15
2.34
1.50
2.96
2.00
3.54
2.00
4.75
2.50
0.251
0.010
0.213
1.65
649
6096
6745
6
9.6
88.6
19.9
1.55
50.0
2CZL
45583
-3
0.071
1,2
18.79
6.6
97.2
1.55
1.61
5.05
4258
0.282
1,2
4.1
93.3
refinement
CNS
1.1
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
SOLVE
hypothetical protein TTHA1568
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol)
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
CME
11
A
CME
11
HELX_P
A
HIS
23
A
HIS
23
1
1
13
A
ASP
38
A
ASP
38
HELX_P
A
GLU
48
A
GLU
48
1
2
11
A
TYR
58
A
TYR
58
HELX_P
A
ALA
62
A
ALA
62
1
3
5
A
THR
106
A
THR
106
HELX_P
A
ALA
116
A
ALA
116
1
4
11
A
ARG
125
A
ARG
125
HELX_P
A
ASP
127
A
ASP
127
5
5
3
A
ARG
128
A
ARG
128
HELX_P
A
GLN
135
A
GLN
135
1
6
8
A
GLU
146
A
GLU
146
HELX_P
A
TYR
151
A
TYR
151
1
7
6
A
PRO
152
A
PRO
152
HELX_P
A
GLY
155
A
GLY
155
5
8
4
A
LEU
162
A
LEU
162
HELX_P
A
GLY
171
A
GLY
171
1
9
10
A
GLY
186
A
GLY
186
HELX_P
A
HIS
207
A
HIS
207
1
10
22
A
PRO
208
A
PRO
208
HELX_P
A
GLU
210
A
GLU
210
5
11
3
A
ALA
211
A
ALA
211
HELX_P
A
ALA
219
A
ALA
219
1
12
9
A
SER
223
A
SER
223
HELX_P
A
VAL
235
A
VAL
235
1
13
13
A
ASN
236
A
ASN
236
HELX_P
A
ASP
241
A
ASP
241
1
14
6
A
VAL
242
A
VAL
242
HELX_P
A
ARG
260
A
ARG
260
1
15
19
covale
1.339
A
PRO
10
A
C
PRO
10
1_555
A
CME
11
A
N
CME
11
1_555
covale
1.336
A
CME
11
A
C
CME
11
1_555
A
PRO
12
A
N
PRO
12
1_555
metalc
2.907
A
K
601
B
K
K
1_555
A
XPE
501
D
O13
XPE
1_555
metalc
2.838
A
K
601
B
K
K
1_555
A
PHE
149
A
O
PHE
149
1_555
metalc
2.920
A
K
601
B
K
K
1_555
A
XPE
501
D
O4
XPE
1_555
metalc
2.885
A
K
601
B
K
K
1_555
A
XPE
501
D
O19
XPE
1_555
metalc
2.905
A
K
601
B
K
K
1_555
A
XPE
501
D
O22
XPE
1_555
metalc
2.959
A
K
601
B
K
K
1_555
A
XPE
501
D
O10
XPE
1_555
metalc
2.907
A
K
601
B
K
K
1_555
A
XPE
501
D
O16
XPE
1_555
metalc
2.831
A
K
601
B
K
K
1_555
A
XPE
501
D
O7
XPE
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Conserved hypothetical protein, TTHA1568, Extremely thermophilic bacteria, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION
YP_144834
GB
1
1
55981537
1
272
2CZL
1
272
55981537
A
1
1
272
5
5
5
parallel
parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
A
LEU
32
A
LEU
32
A
LEU
36
A
LEU
36
A
LEU
4
A
LEU
4
A
PHE
8
A
PHE
8
A
LEU
53
A
LEU
53
A
SER
57
A
SER
57
A
LEU
174
A
LEU
174
A
ARG
182
A
ARG
182
A
TYR
68
A
TYR
68
A
ALA
70
A
ALA
70
A
LEU
32
A
LEU
32
A
LEU
36
A
LEU
36
A
LEU
4
A
LEU
4
A
PHE
8
A
PHE
8
A
LEU
53
A
LEU
53
A
SER
57
A
SER
57
A
LEU
174
A
LEU
174
A
ARG
182
A
ARG
182
A
ALA
76
A
ALA
76
A
GLY
78
A
GLY
78
A
VAL
120
A
VAL
120
A
GLU
123
A
GLU
123
A
ARG
98
A
ARG
98
A
VAL
101
A
VAL
101
A
ALA
140
A
ALA
140
A
ILE
143
A
ILE
143
A
LEU
84
A
LEU
84
A
ALA
87
A
ALA
87
A
VAL
157
A
VAL
157
A
ASP
161
A
ASP
161
BINDING SITE FOR RESIDUE K A 601
Software
2
BINDING SITE FOR RESIDUE TLA A 401
Software
11
BINDING SITE FOR RESIDUE XPE A 501
Software
10
A
PHE
149
A
PHE
149
2
1_555
A
XPE
501
D
XPE
2
1_555
A
VAL
39
A
VAL
39
11
1_555
A
LYS
55
A
LYS
55
11
1_555
A
SER
57
A
SER
57
11
1_555
A
THR
106
A
THR
106
11
1_555
A
THR
107
A
THR
107
11
1_555
A
ALA
108
A
ALA
108
11
1_555
A
HIS
145
A
HIS
145
11
1_555
A
LEU
176
A
LEU
176
11
1_555
A
HOH
602
E
HOH
11
1_555
A
HOH
648
E
HOH
11
1_555
A
HOH
696
E
HOH
11
1_555
A
ARG
148
A
ARG
148
10
1_555
A
PHE
149
A
PHE
149
10
1_555
A
TYR
151
A
TYR
151
10
1_555
A
PRO
152
A
PRO
152
10
1_555
A
ARG
153
A
ARG
153
10
1_555
A
ARG
198
A
ARG
198
10
5_645
A
GLU
225
A
GLU
225
10
1_555
A
ALA
229
A
ALA
229
10
1_555
A
K
601
B
K
10
1_555
A
HOH
844
E
HOH
10
1_555
96
P 43 21 2