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- PDB-6fps: Crystal structure of 4-oxalocrotonate tautomerase triple mutant L... -

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Basic information

Entry
Database: PDB / ID: 6fps
TitleCrystal structure of 4-oxalocrotonate tautomerase triple mutant L8Y/M45Y/F50A
Components2-hydroxymuconate tautomerase
KeywordsISOMERASE / 2-hydroxymuconate tautomerase
Function / homology
Function and homology information


xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPijning, T. / Thunnissen, A.M.W.H.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
European Research Council - European Union Horizon 2020 research and innovation Programme635595 Netherlands
European Research Council - European Union Horizon 2020 research and innovation Programme713483 Netherlands
CitationJournal: ACS Catal / Year: 2019
Title: Enantioselective Synthesis of Pharmaceutically Active gamma-Aminobutyric Acids Using a Tailor-Made Artificial Michaelase in One-Pot Cascade Reactions.
Authors: Biewenga, L. / Saravanan, T. / Kunzendorf, A. / van der Meer, J.Y. / Pijning, T. / Tepper, P.G. / van Merkerk, R. / Charnock, S.J. / Thunnissen, A.W.H. / Poelarends, G.J.
History
DepositionFeb 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
D: 2-hydroxymuconate tautomerase
E: 2-hydroxymuconate tautomerase
F: 2-hydroxymuconate tautomerase
G: 2-hydroxymuconate tautomerase
H: 2-hydroxymuconate tautomerase
I: 2-hydroxymuconate tautomerase
J: 2-hydroxymuconate tautomerase
K: 2-hydroxymuconate tautomerase
L: 2-hydroxymuconate tautomerase
M: 2-hydroxymuconate tautomerase
N: 2-hydroxymuconate tautomerase
O: 2-hydroxymuconate tautomerase
P: 2-hydroxymuconate tautomerase
Q: 2-hydroxymuconate tautomerase
R: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,08620
Polymers122,89918
Non-polymers1872
Water6,143341
1
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
D: 2-hydroxymuconate tautomerase
E: 2-hydroxymuconate tautomerase
F: 2-hydroxymuconate tautomerase


Theoretical massNumber of molelcules
Total (without water)40,9666
Polymers40,9666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-63 kcal/mol
Surface area14670 Å2
MethodPISA
2
G: 2-hydroxymuconate tautomerase
H: 2-hydroxymuconate tautomerase
I: 2-hydroxymuconate tautomerase
J: 2-hydroxymuconate tautomerase
K: 2-hydroxymuconate tautomerase
L: 2-hydroxymuconate tautomerase


Theoretical massNumber of molelcules
Total (without water)40,9666
Polymers40,9666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-57 kcal/mol
Surface area14860 Å2
MethodPISA
3
M: 2-hydroxymuconate tautomerase
N: 2-hydroxymuconate tautomerase
O: 2-hydroxymuconate tautomerase
P: 2-hydroxymuconate tautomerase
Q: 2-hydroxymuconate tautomerase
R: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1538
Polymers40,9666
Non-polymers1872
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-62 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.046, 99.509, 118.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216Q
117A
217R
118B
218C
119B
219D
120B
220E
121B
221F
122B
222G
123B
223H
124B
224I
125B
225J
126B
226K
127B
227L
128B
228M
129B
229N
130B
230O
131B
231P
132B
232Q
133B
233R
134C
234D
135C
235E
136C
236F
137C
237G
138C
238H
139C
239I
140C
240J
141C
241K
142C
242L
143C
243M
144C
244N
145C
245O
146C
246P
147C
247Q
148C
248R
149D
249E
150D
250F
151D
251G
152D
252H
153D
253I
154D
254J
155D
255K
156D
256L
157D
257M
158D
258N
159D
259O
160D
260P
161D
261Q
162D
262R
163E
263F
164E
264G
165E
265H
166E
266I
167E
267J
168E
268K
169E
269L
170E
270M
171E
271N
172E
272O
173E
273P
174E
274Q
175E
275R
176F
276G
177F
277H
178F
278I
179F
279J
180F
280K
181F
281L
182F
282M
183F
283N
184F
284O
185F
285P
186F
286Q
187F
287R
188G
288H
189G
289I
190G
290J
191G
291K
192G
292L
193G
293M
194G
294N
195G
295O
196G
296P
197G
297Q
198G
298R
199H
299I
1100H
2100J
1101H
2101K
1102H
2102L
1103H
2103M
1104H
2104N
1105H
2105O
1106H
2106P
1107H
2107Q
1108H
2108R
1109I
2109J
1110I
2110K
1111I
2111L
1112I
2112M
1113I
2113N
1114I
2114O
1115I
2115P
1116I
2116Q
1117I
2117R
1118J
2118K
1119J
2119L
1120J
2120M
1121J
2121N
1122J
2122O
1123J
2123P
1124J
2124Q
1125J
2125R
1126K
2126L
1127K
2127M
1128K
2128N
1129K
2129O
1130K
2130P
1131K
2131Q
1132K
2132R
1133L
2133M
1134L
2134N
1135L
2135O
1136L
2136P
1137L
2137Q
1138L
2138R
1139M
2139N
1140M
2140O
1141M
2141P
1142M
2142Q
1143M
2143R
1144N
2144O
1145N
2145P
1146N
2146Q
1147N
2147R
1148O
2148P
1149O
2149Q
1150O
2150R
1151P
2151Q
1152P
2152R
1153Q
2153R

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA1 - 571 - 57
21ALAALABB1 - 571 - 57
12LYSLYSAA1 - 591 - 59
22LYSLYSCC1 - 591 - 59
13LYSLYSAA1 - 591 - 59
23LYSLYSDD1 - 591 - 59
14SERSERAA1 - 581 - 58
24SERSEREE1 - 581 - 58
15ALAALAAA1 - 571 - 57
25ALAALAFF1 - 571 - 57
16SERSERAA1 - 581 - 58
26SERSERGG1 - 581 - 58
17LYSLYSAA1 - 591 - 59
27LYSLYSHH1 - 591 - 59
18LYSLYSAA1 - 591 - 59
28LYSLYSII1 - 591 - 59
19SERSERAA1 - 581 - 58
29SERSERJJ1 - 581 - 58
110LYSLYSAA1 - 591 - 59
210LYSLYSKK1 - 591 - 59
111ALAALAAA1 - 571 - 57
211ALAALALL1 - 571 - 57
112LYSLYSAA1 - 591 - 59
212LYSLYSMM1 - 591 - 59
113SERSERAA1 - 581 - 58
213SERSERNN1 - 581 - 58
114ALAALAAA1 - 571 - 57
214ALAALAOO1 - 571 - 57
115SERSERAA1 - 581 - 58
215SERSERPP1 - 581 - 58
116SERSERAA1 - 581 - 58
216SERSERQQ1 - 581 - 58
117ALAALAAA1 - 571 - 57
217ALAALARR1 - 571 - 57
118ALAALABB1 - 571 - 57
218ALAALACC1 - 571 - 57
119ALAALABB1 - 571 - 57
219ALAALADD1 - 571 - 57
120ALAALABB1 - 571 - 57
220ALAALAEE1 - 571 - 57
121SERSERBB1 - 581 - 58
221SERSERFF1 - 581 - 58
122ALAALABB1 - 571 - 57
222ALAALAGG1 - 571 - 57
123ALAALABB1 - 571 - 57
223ALAALAHH1 - 571 - 57
124ALAALABB1 - 571 - 57
224ALAALAII1 - 571 - 57
125ALAALABB1 - 571 - 57
225ALAALAJJ1 - 571 - 57
126ALAALABB1 - 571 - 57
226ALAALAKK1 - 571 - 57
127SERSERBB1 - 581 - 58
227SERSERLL1 - 581 - 58
128ALAALABB1 - 571 - 57
228ALAALAMM1 - 571 - 57
129ALAALABB1 - 571 - 57
229ALAALANN1 - 571 - 57
130SERSERBB1 - 581 - 58
230SERSEROO1 - 581 - 58
131ALAALABB1 - 571 - 57
231ALAALAPP1 - 571 - 57
132ALAALABB1 - 571 - 57
232ALAALAQQ1 - 571 - 57
133SERSERBB1 - 581 - 58
233SERSERRR1 - 581 - 58
134LYSLYSCC1 - 591 - 59
234LYSLYSDD1 - 591 - 59
135SERSERCC1 - 581 - 58
235SERSEREE1 - 581 - 58
136ALAALACC1 - 571 - 57
236ALAALAFF1 - 571 - 57
137SERSERCC1 - 581 - 58
237SERSERGG1 - 581 - 58
138LYSLYSCC1 - 591 - 59
238LYSLYSHH1 - 591 - 59
139LYSLYSCC1 - 591 - 59
239LYSLYSII1 - 591 - 59
140SERSERCC1 - 581 - 58
240SERSERJJ1 - 581 - 58
141LYSLYSCC1 - 591 - 59
241LYSLYSKK1 - 591 - 59
142ALAALACC1 - 571 - 57
242ALAALALL1 - 571 - 57
143LYSLYSCC1 - 591 - 59
243LYSLYSMM1 - 591 - 59
144SERSERCC1 - 581 - 58
244SERSERNN1 - 581 - 58
145ALAALACC1 - 571 - 57
245ALAALAOO1 - 571 - 57
146SERSERCC1 - 581 - 58
246SERSERPP1 - 581 - 58
147SERSERCC1 - 581 - 58
247SERSERQQ1 - 581 - 58
148ALAALACC1 - 571 - 57
248ALAALARR1 - 571 - 57
149SERSERDD1 - 581 - 58
249SERSEREE1 - 581 - 58
150ALAALADD1 - 571 - 57
250ALAALAFF1 - 571 - 57
151SERSERDD1 - 581 - 58
251SERSERGG1 - 581 - 58
152LYSLYSDD1 - 591 - 59
252LYSLYSHH1 - 591 - 59
153LYSLYSDD1 - 591 - 59
253LYSLYSII1 - 591 - 59
154SERSERDD1 - 581 - 58
254SERSERJJ1 - 581 - 58
155LYSLYSDD1 - 591 - 59
255LYSLYSKK1 - 591 - 59
156ALAALADD1 - 571 - 57
256ALAALALL1 - 571 - 57
157LYSLYSDD1 - 591 - 59
257LYSLYSMM1 - 591 - 59
158SERSERDD1 - 581 - 58
258SERSERNN1 - 581 - 58
159ALAALADD1 - 571 - 57
259ALAALAOO1 - 571 - 57
160SERSERDD1 - 581 - 58
260SERSERPP1 - 581 - 58
161SERSERDD1 - 581 - 58
261SERSERQQ1 - 581 - 58
162ALAALADD1 - 571 - 57
262ALAALARR1 - 571 - 57
163ALAALAEE1 - 571 - 57
263ALAALAFF1 - 571 - 57
164VALVALEE1 - 601 - 60
264VALVALGG1 - 601 - 60
165SERSEREE1 - 581 - 58
265SERSERHH1 - 581 - 58
166SERSEREE1 - 581 - 58
266SERSERII1 - 581 - 58
167VALVALEE1 - 601 - 60
267VALVALJJ1 - 601 - 60
168SERSEREE1 - 581 - 58
268SERSERKK1 - 581 - 58
169ALAALAEE1 - 571 - 57
269ALAALALL1 - 571 - 57
170SERSEREE1 - 581 - 58
270SERSERMM1 - 581 - 58
171LYSLYSEE1 - 591 - 59
271LYSLYSNN1 - 591 - 59
172ALAALAEE1 - 571 - 57
272ALAALAOO1 - 571 - 57
173LYSLYSEE1 - 591 - 59
273LYSLYSPP1 - 591 - 59
174LYSLYSEE1 - 591 - 59
274LYSLYSQQ1 - 591 - 59
175ALAALAEE1 - 571 - 57
275ALAALARR1 - 571 - 57
176ALAALAFF1 - 571 - 57
276ALAALAGG1 - 571 - 57
177ALAALAFF1 - 571 - 57
277ALAALAHH1 - 571 - 57
178ALAALAFF1 - 571 - 57
278ALAALAII1 - 571 - 57
179ALAALAFF1 - 571 - 57
279ALAALAJJ1 - 571 - 57
180ALAALAFF1 - 571 - 57
280ALAALAKK1 - 571 - 57
181SERSERFF1 - 581 - 58
281SERSERLL1 - 581 - 58
182ALAALAFF1 - 571 - 57
282ALAALAMM1 - 571 - 57
183ALAALAFF1 - 571 - 57
283ALAALANN1 - 571 - 57
184SERSERFF1 - 581 - 58
284SERSEROO1 - 581 - 58
185ALAALAFF1 - 571 - 57
285ALAALAPP1 - 571 - 57
186ALAALAFF1 - 571 - 57
286ALAALAQQ1 - 571 - 57
187SERSERFF1 - 581 - 58
287SERSERRR1 - 581 - 58
188SERSERGG1 - 581 - 58
288SERSERHH1 - 581 - 58
189SERSERGG1 - 581 - 58
289SERSERII1 - 581 - 58
190VALVALGG1 - 601 - 60
290VALVALJJ1 - 601 - 60
191SERSERGG1 - 581 - 58
291SERSERKK1 - 581 - 58
192ALAALAGG1 - 571 - 57
292ALAALALL1 - 571 - 57
193SERSERGG1 - 581 - 58
293SERSERMM1 - 581 - 58
194LYSLYSGG1 - 591 - 59
294LYSLYSNN1 - 591 - 59
195ALAALAGG1 - 571 - 57
295ALAALAOO1 - 571 - 57
196LYSLYSGG1 - 591 - 59
296LYSLYSPP1 - 591 - 59
197LYSLYSGG1 - 591 - 59
297LYSLYSQQ1 - 591 - 59
198ALAALAGG1 - 571 - 57
298ALAALARR1 - 571 - 57
199LYSLYSHH1 - 591 - 59
299LYSLYSII1 - 591 - 59
1100SERSERHH1 - 581 - 58
2100SERSERJJ1 - 581 - 58
1101LYSLYSHH1 - 591 - 59
2101LYSLYSKK1 - 591 - 59
1102ALAALAHH1 - 571 - 57
2102ALAALALL1 - 571 - 57
1103LYSLYSHH1 - 591 - 59
2103LYSLYSMM1 - 591 - 59
1104SERSERHH1 - 581 - 58
2104SERSERNN1 - 581 - 58
1105ALAALAHH1 - 571 - 57
2105ALAALAOO1 - 571 - 57
1106SERSERHH1 - 581 - 58
2106SERSERPP1 - 581 - 58
1107SERSERHH1 - 581 - 58
2107SERSERQQ1 - 581 - 58
1108ALAALAHH1 - 571 - 57
2108ALAALARR1 - 571 - 57
1109SERSERII1 - 581 - 58
2109SERSERJJ1 - 581 - 58
1110LYSLYSII1 - 591 - 59
2110LYSLYSKK1 - 591 - 59
1111ALAALAII1 - 571 - 57
2111ALAALALL1 - 571 - 57
1112LYSLYSII1 - 591 - 59
2112LYSLYSMM1 - 591 - 59
1113SERSERII1 - 581 - 58
2113SERSERNN1 - 581 - 58
1114ALAALAII1 - 571 - 57
2114ALAALAOO1 - 571 - 57
1115SERSERII1 - 581 - 58
2115SERSERPP1 - 581 - 58
1116SERSERII1 - 581 - 58
2116SERSERQQ1 - 581 - 58
1117ALAALAII1 - 571 - 57
2117ALAALARR1 - 571 - 57
1118SERSERJJ1 - 581 - 58
2118SERSERKK1 - 581 - 58
1119ALAALAJJ1 - 571 - 57
2119ALAALALL1 - 571 - 57
1120SERSERJJ1 - 581 - 58
2120SERSERMM1 - 581 - 58
1121LYSLYSJJ1 - 591 - 59
2121LYSLYSNN1 - 591 - 59
1122ALAALAJJ1 - 571 - 57
2122ALAALAOO1 - 571 - 57
1123LYSLYSJJ1 - 591 - 59
2123LYSLYSPP1 - 591 - 59
1124LYSLYSJJ1 - 591 - 59
2124LYSLYSQQ1 - 591 - 59
1125ALAALAJJ1 - 571 - 57
2125ALAALARR1 - 571 - 57
1126ALAALAKK1 - 571 - 57
2126ALAALALL1 - 571 - 57
1127LYSLYSKK1 - 591 - 59
2127LYSLYSMM1 - 591 - 59
1128SERSERKK1 - 581 - 58
2128SERSERNN1 - 581 - 58
1129ALAALAKK1 - 571 - 57
2129ALAALAOO1 - 571 - 57
1130SERSERKK1 - 581 - 58
2130SERSERPP1 - 581 - 58
1131SERSERKK1 - 581 - 58
2131SERSERQQ1 - 581 - 58
1132ALAALAKK1 - 571 - 57
2132ALAALARR1 - 571 - 57
1133ALAALALL1 - 571 - 57
2133ALAALAMM1 - 571 - 57
1134ALAALALL1 - 571 - 57
2134ALAALANN1 - 571 - 57
1135SERSERLL1 - 581 - 58
2135SERSEROO1 - 581 - 58
1136ALAALALL1 - 571 - 57
2136ALAALAPP1 - 571 - 57
1137ALAALALL1 - 571 - 57
2137ALAALAQQ1 - 571 - 57
1138SERSERLL1 - 581 - 58
2138SERSERRR1 - 581 - 58
1139SERSERMM1 - 581 - 58
2139SERSERNN1 - 581 - 58
1140ALAALAMM1 - 571 - 57
2140ALAALAOO1 - 571 - 57
1141SERSERMM1 - 581 - 58
2141SERSERPP1 - 581 - 58
1142SERSERMM1 - 581 - 58
2142SERSERQQ1 - 581 - 58
1143ALAALAMM1 - 571 - 57
2143ALAALARR1 - 571 - 57
1144ALAALANN1 - 571 - 57
2144ALAALAOO1 - 571 - 57
1145ARGARGNN1 - 621 - 62
2145ARGARGPP1 - 621 - 62
1146ARGARGNN1 - 621 - 62
2146ARGARGQQ1 - 621 - 62
1147ALAALANN1 - 571 - 57
2147ALAALARR1 - 571 - 57
1148ALAALAOO1 - 571 - 57
2148ALAALAPP1 - 571 - 57
1149ALAALAOO1 - 571 - 57
2149ALAALAQQ1 - 571 - 57
1150SERSEROO1 - 581 - 58
2150SERSERRR1 - 581 - 58
1151ARGARGPP1 - 621 - 62
2151ARGARGQQ1 - 621 - 62
1152ALAALAPP1 - 571 - 57
2152ALAALARR1 - 571 - 57
1153ALAALAQQ1 - 571 - 57
2153ALAALARR1 - 571 - 57

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153

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Components

#1: Protein
2-hydroxymuconate tautomerase / 4-oxalocrotonate tautomerase / 4-OT


Mass: 6827.736 Da / Num. of mol.: 18 / Mutation: L8Y, M45Y, F50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M bistris-propane HCl, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033216 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033216 Å / Relative weight: 1
ReflectionResolution: 1.9→45.86 Å / Num. obs: 84372 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Net I/σ(I): 14.2 / Num. measured all: 685428 / Scaling rejects: 75
Reflection shell

Diffraction-ID: 1 / Redundancy: 7.7 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.931.52644170.7420.5861.637100
10.05-45.860.02566110.0090.02799.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å45.86 Å
Translation1.9 Å45.86 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0210refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 4X19
Resolution: 1.9→45.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.982 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.141
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 4096 4.9 %RANDOM
Rwork0.2005 ---
obs0.2016 80195 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 119.65 Å2 / Biso mean: 39.268 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.95 Å20 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 1.9→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 11 341 8518
Biso mean--52.2 38.74 -
Num. residues----1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198401
X-RAY DIFFRACTIONr_bond_other_d0.0010.028160
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9711332
X-RAY DIFFRACTIONr_angle_other_deg0.847318909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68551087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62223.579366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.749151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6911581
X-RAY DIFFRACTIONr_chiral_restr0.1030.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021595
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A15640.06
12B15640.06
21A15820.08
22C15820.08
31A16190.05
32D16190.05
41A15770.06
42E15770.06
51A15520.07
52F15520.07
61A15790.09
62G15790.09
71A16160.07
72H16160.07
81A16140.07
82I16140.07
91A15850.06
92J15850.06
101A16110.06
102K16110.06
111A15120.07
112L15120.07
121A15930.08
122M15930.08
131A15620.09
132N15620.09
141A15450.08
142O15450.08
151A15720.06
152P15720.06
161A15480.07
162Q15480.07
171A15290.08
172R15290.08
181B15180.08
182C15180.08
191B15600.04
192D15600.04
201B15440.06
202E15440.06
211B16190.04
212F16190.04
221B15390.08
222G15390.08
231B15600.05
232H15600.05
241B15520.07
242I15520.07
251B15700.04
252J15700.04
261B15390.06
262K15390.06
271B15560.06
272L15560.06
281B15360.07
282M15360.07
291B15450.07
292N15450.07
301B15900.05
302O15900.05
311B15400.06
312P15400.06
321B15190.06
322Q15190.06
331B15670.07
332R15670.07
341C15770.08
342D15770.08
351C15360.08
352E15360.08
361C15290.08
362F15290.08
371C15520.09
372G15520.09
381C15940.07
382H15940.07
391C15970.07
392I15970.07
401C15450.08
402J15450.08
411C15740.07
412K15740.07
421C15210.06
422L15210.06
431C15660.09
432M15660.09
441C15860.06
442N15860.06
451C15280.08
452O15280.08
461C15560.07
462P15560.07
471C15380.07
472Q15380.07
481C15340.07
482R15340.07
491D15680.06
492E15680.06
501D15690.06
502F15690.06
511D15780.09
512G15780.09
521D16480.05
522H16480.05
531D16180.07
532I16180.07
541D16000.04
542J16000.04
551D15940.06
552K15940.06
561D15320.06
562L15320.06
571D16120.07
572M16120.07
581D15910.07
582N15910.07
591D15750.07
592O15750.07
601D15810.05
602P15810.05
611D15540.06
612Q15540.06
621D15510.07
622R15510.07
631E15290.07
632F15290.07
641E16050.09
642G16050.09
651E15420.07
652H15420.07
661E15640.06
662I15640.06
671E16170.06
672J16170.06
681E15650.04
682K15650.04
691E14910.07
692L14910.07
701E15540.06
702M15540.06
711E15540.09
712N15540.09
721E15090.08
722O15090.08
731E15810.06
732P15810.06
741E15530.06
742Q15530.06
751E15010.08
752R15010.08
761F15280.09
762G15280.09
771F15480.06
772H15480.06
781F15400.07
782I15400.07
791F15720.05
792J15720.05
801F15250.07
802K15250.07
811F15690.06
812L15690.06
821F15260.08
822M15260.08
831F15510.06
832N15510.06
841F15840.06
842O15840.06
851F15370.06
852P15370.06
861F15140.06
862Q15140.06
871F15740.06
872R15740.06
881G15750.09
882H15750.09
891G15970.07
892I15970.07
901G16130.1
902J16130.1
911G15780.07
912K15780.07
921G14930.1
922L14930.1
931G15740.08
932M15740.08
941G15870.1
942N15870.1
951G15440.09
952O15440.09
961G15940.08
962P15940.08
971G15790.08
972Q15790.08
981G15330.09
982R15330.09
991H16200.06
992I16200.06
1001H15820.05
1002J15820.05
1011H15980.05
1012K15980.05
1021H15140.07
1022L15140.07
1031H15980.08
1032M15980.08
1041H15860.06
1042N15860.06
1051H15690.05
1052O15690.05
1061H15820.04
1062P15820.04
1071H15550.05
1072Q15550.05
1081H15460.06
1082R15460.06
1091I15770.06
1092J15770.06
1101I16230.04
1102K16230.04
1111I15100.07
1112L15100.07
1121I16090.06
1122M16090.06
1131I15770.07
1132N15770.07
1141I15590.06
1142O15590.06
1151I15810.05
1152P15810.05
1161I15600.06
1162Q15600.06
1171I15490.07
1172R15490.07
1181J15810.06
1182K15810.06
1191J15480.06
1192L15480.06
1201J15890.07
1202M15890.07
1211J16220.08
1212N16220.08
1221J15820.06
1222O15820.06
1231J16230.06
1232P16230.06
1241J15880.07
1242Q15880.07
1251J15520.07
1252R15520.07
1261K14910.07
1262L14910.07
1271K15830.06
1272M15830.06
1281K15410.07
1282N15410.07
1291K15240.06
1292O15240.06
1301K15620.04
1302P15620.04
1311K15420.05
1312Q15420.05
1321K15110.07
1322R15110.07
1331L15100.08
1332M15100.08
1341L15310.06
1342N15310.06
1351L15410.08
1352O15410.08
1361L15150.06
1362P15150.06
1371L15010.06
1372Q15010.06
1381L15470.07
1382R15470.07
1391M15680.09
1392N15680.09
1401M15690.08
1402O15690.08
1411M15740.08
1412P15740.08
1421M15560.08
1422Q15560.08
1431M15580.08
1432R15580.08
1441N15760.07
1442O15760.07
1451N16970.1
1452P16970.1
1461N16920.09
1462Q16920.09
1471N15720.07
1472R15720.07
1481O15450.06
1482P15450.06
1491O15230.06
1492Q15230.06
1501O15960.05
1502R15960.05
1511P17000.05
1512Q17000.05
1521P15440.06
1522R15440.06
1531Q15130.06
1532R15130.06
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 307 -
Rwork0.316 5870 -
all-6177 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.32031.9113-1.31164.6431-0.53243.4873-0.21610.1406-0.286-0.27420.0162-0.16110.16890.07480.19990.03820.02120.02260.0953-0.03260.04273.566-3.326-48.858
22.4784-0.7268-0.51353.1015-0.09714.9677-0.0917-0.18080.02630.1946-0.0483-0.0020.0294-0.02960.13990.0316-0.01560.00840.1016-0.04040.0422.11-3.114-37.588
32.2482-1.1719-0.22233.0119-0.56152.2430.11360.23710.029-0.3241-0.13730.2201-0.197-0.22370.02370.1058-0.0128-0.03340.1667-0.04770.0554-12.6359.306-50.238
42.45680.8175-0.01582.31561.2933.43060.0084-0.10080.00420.0123-0.0070.0331-0.0324-0.1735-0.00140.067-0.0258-0.02670.111-0.00680.0169-12.30411.928-38.82
53.16680.3863-0.09541.76370.062.9394-0.01580.20080.1971-0.11520.0209-0.0544-0.31120.2907-0.00510.1496-0.05980.00380.1412-0.01630.02536.40417.14-50.377
61.84510.21070.15682.41441.47743.24310.0011-0.04560.0172-0.022-0.0061-0.0256-0.48290.08860.0050.1102-0.03290.00810.1241-0.02830.01797.58517.046-38.866
72.3611-1.83750.68595.2986-1.33752.5561-0.0279-0.24820.09960.43460.0604-0.1896-0.3040.0722-0.03250.0902-0.0245-0.00930.1387-0.02880.0146-36.208-2.707-19.496
83.28150.29751.69051.7871-0.32723.7620.03840.0750.1054-0.0367-0.0069-0.0263-0.15030.0281-0.03150.05690.0080.00450.096-0.02580.0164-38.544-0.995-30.984
92.29691.1343-0.87442.475-0.72693.91190.048-0.04890.0949-0.01360.03590.25610.2224-0.6331-0.08390.1239-0.0044-0.00750.26890.02370.0294-54.383-12.783-19.608
103.0122-1.0450.32012.41460.39594.79540.0398-0.06-0.07310.0885-0.02060.13920.0013-0.5844-0.01920.0798-0.02920.010.21660.01510.01-54.448-14.438-31.481
115.4336-0.205-1.43922.0273-0.05184.2087-0.0332-0.2726-0.30330.2551-0.0434-0.13710.19660.33110.07660.0967-0.0264-0.03380.1370.04410.0368-36.509-23.326-20.698
121.82660.6673-0.77914.0926-0.3923.92880.01080.0255-0.0033-0.1106-0.067-0.12420.0520.15720.05630.0433-0.0125-0.02180.13850.02330.0243-35.491-21.927-32.143
131.52430.47080.06462.6744-0.76063.16770.0362-0.1856-0.0640.0442-0.0851-0.1334-0.16950.28940.04890.0535-0.0285-0.00350.1374-0.0080.0129.27315.2850.487
142.9269-1.1762-0.37021.6247-0.17482.81090.01910.03370.1-0.0153-0.0071-0.19950.00290.3778-0.01190.0706-0.0561-0.00250.1151-0.01360.0357.99417.412-11.923
154.13881.13990.38991.56190.39812.4282-0.1058-0.12840.20160.00870.04340.1206-0.036-0.17720.06230.0455-0.0247-0.00390.0745-0.00110.0139-11.72117.712-0.397
160.98570.04070.01013.9783-0.03081.80970.02310.03010.0383-0.1069-0.02020.2-0.0443-0.092-0.00280.0256-0.0384-0.00280.0987-0.00640.0128-12.77514.834-12.097
173.1404-1.3955-0.23232.1321-0.36591.4407-0.103-0.0315-0.23720.09880.0844-0.00020.27790.12550.01860.0919-0.0232-0.00050.1772-0.01290.0264-4.663-1.1611.434
184.58841.276-0.59922.0285-0.06543.22530.0376-0.1372-0.1747-0.0561-0.0418-0.05310.2013-0.08170.00410.05290.0079-0.00730.13560.00060.0075-1.929-2.114-10.239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 59
2X-RAY DIFFRACTION2B1 - 58
3X-RAY DIFFRACTION3C1 - 59
4X-RAY DIFFRACTION4D1 - 59
5X-RAY DIFFRACTION5E1 - 60
6X-RAY DIFFRACTION6F1 - 58
7X-RAY DIFFRACTION7G1 - 60
8X-RAY DIFFRACTION8H1 - 59
9X-RAY DIFFRACTION9I1 - 59
10X-RAY DIFFRACTION10J1 - 60
11X-RAY DIFFRACTION11K1 - 59
12X-RAY DIFFRACTION12L1 - 58
13X-RAY DIFFRACTION13M1 - 59
14X-RAY DIFFRACTION14N1 - 62
15X-RAY DIFFRACTION15O1 - 58
16X-RAY DIFFRACTION16P1 - 62
17X-RAY DIFFRACTION17Q1 - 62
18X-RAY DIFFRACTION18R1 - 58

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