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- PDB-7qxf: Fructose-6-phosphate aldolase (FSA) mutant R134V, S166G, with cov... -

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Basic information

Entry
Database: PDB / ID: 7qxf
TitleFructose-6-phosphate aldolase (FSA) mutant R134V, S166G, with covalently bound active site ligand
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / mutant protein engineering aldol addition
Function / homology
Function and homology information


ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsDobritzsch, D. / Widersten, M. / Engel, S.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Other private194-0638
Other private183-358
Other private2019-01-24 Sweden
Citation
Journal: Catalysis Science And Technology / Year: 2023
Title: Engineered aldolases catalyzing stereoselective aldol reactions between aryl-substituted ketones and aldehydes
Authors: Cornelius, E.C. / Bartl, M. / Persson, L.J. / Xiong, R. / Cederfelt, D. / Rad, F.M. / Norberg, T. / Engel, S. / Marklund, E.G. / Dobritzsch, D. / Widersten, M.
#1: Journal: Biochemistry / Year: 2018
Title: New Stereoselective Biocatalysts for Carboligation and Retro-Aldol Cleavage Reactions Derived from d-Fructose 6-Phosphate Aldolase.
Authors: Ma, H. / Engel, S. / Enugala, T.R. / Al-Smadi, D. / Gautier, C. / Widersten, M.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-6-phosphate aldolase 1
B: Fructose-6-phosphate aldolase 1
C: Fructose-6-phosphate aldolase 1
D: Fructose-6-phosphate aldolase 1
E: Fructose-6-phosphate aldolase 1
F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1
K: Fructose-6-phosphate aldolase 1
L: Fructose-6-phosphate aldolase 1
M: Fructose-6-phosphate aldolase 1
N: Fructose-6-phosphate aldolase 1
O: Fructose-6-phosphate aldolase 1


Theoretical massNumber of molelcules
Total (without water)359,08115
Polymers359,08115
Non-polymers00
Water3,189177
1
A: Fructose-6-phosphate aldolase 1
B: Fructose-6-phosphate aldolase 1
C: Fructose-6-phosphate aldolase 1
D: Fructose-6-phosphate aldolase 1
E: Fructose-6-phosphate aldolase 1
K: Fructose-6-phosphate aldolase 1
L: Fructose-6-phosphate aldolase 1
M: Fructose-6-phosphate aldolase 1
N: Fructose-6-phosphate aldolase 1
O: Fructose-6-phosphate aldolase 1


Theoretical massNumber of molelcules
Total (without water)239,38710
Polymers239,38710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39480 Å2
ΔGint-328 kcal/mol
Surface area70020 Å2
MethodPISA
2
F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1

F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1


Theoretical massNumber of molelcules
Total (without water)239,38710
Polymers239,38710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area39700 Å2
ΔGint-334 kcal/mol
Surface area69860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.198, 176.865, 120.093
Angle α, β, γ (deg.)90.000, 91.500, 90.000
Int Tables number5
Space group name H-MC121
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
215B
116A
216C
117A
217D
118A
218E
119A
219F
120A
220G
121A
221H
122A
222I
123A
223J
124A
224K
125A
225L
126A
226M
127A
227N
128A
228O
129B
229C
130B
230D
131B
231E
132B
232F
133B
233G
134B
234H
135B
235I
136B
236J
137B
237K
138B
238L
139B
239M
140B
240N
141B
241O
142B
242C
143B
243D
144B
244E
145B
245F
146B
246G
147B
247H
148B
248I
149B
249J
150B
250K
151B
251L
152B
252M
153B
253N
154B
254O
155C
255D
156C
256E
157C
257F
158C
258G
159C
259H
160C
260I
161C
261J
162C
262K
163C
263L
164C
264M
165C
265N
166C
266O
167C
267D
168C
268E
169C
269F
170C
270G
171C
271H
172C
272I
173C
273J
174C
274K
175C
275L
176C
276M
177C
277N
178C
278O
179D
279E
180D
280F
181D
281G
182D
282H
183D
283I
184D
284J
185D
285K
186D
286L
187D
287M
188D
288N
189D
289O
190D
290E
191D
291F
192D
292G
193D
293H
194D
294I
195D
295J
196D
296K
197D
297L
198D
298M
199D
299N
1100D
2100O
1101E
2101F
1102E
2102G
1103E
2103H
1104E
2104I
1105E
2105J
1106E
2106K
1107E
2107L
1108E
2108M
1109E
2109N
1110E
2110O
1111E
2111F
1112E
2112G
1113E
2113H
1114E
2114I
1115E
2115J
1116E
2116K
1117E
2117L
1118E
2118M
1119E
2119N
1120E
2120O
1121F
2121G
1122F
2122H
1123F
2123I
1124F
2124J
1125F
2125K
1126F
2126L
1127F
2127M
1128F
2128N
1129F
2129O
1130F
2130G
1131F
2131H
1132F
2132I
1133F
2133J
1134F
2134K
1135F
2135L
1136F
2136M
1137F
2137N
1138F
2138O
1139G
2139H
1140G
2140I
1141G
2141J
1142G
2142K
1143G
2143L
1144G
2144M
1145G
2145N
1146G
2146O
1147G
2147H
1148G
2148I
1149G
2149J
1150G
2150K
1151G
2151L
1152G
2152M
1153G
2153N
1154G
2154O
1155H
2155I
1156H
2156J
1157H
2157K
1158H
2158L
1159H
2159M
1160H
2160N
1161H
2161O
1162H
2162I
1163H
2163J
1164H
2164K
1165H
2165L
1166H
2166M
1167H
2167N
1168H
2168O
1169I
2169J
1170I
2170K
1171I
2171L
1172I
2172M
1173I
2173N
1174I
2174O
1175I
2175J
1176I
2176K
1177I
2177L
1178I
2178M
1179I
2179N
1180I
2180O
1181J
2181K
1182J
2182L
1183J
2183M
1184J
2184N
1185J
2185O
1186J
2186K
1187J
2187L
1188J
2188M
1189J
2189N
1190J
2190O
1191K
2191L
1192K
2192M
1193K
2193N
1194K
2194O
1195K
2195L
1196K
2196M
1197K
2197N
1198K
2198O
1199L
2199M
1200L
2200N
1201L
2201O
1202L
2202M
1203L
2203N
1204L
2204O
1205M
2205N
1206M
2206O
1207M
2207N
1208M
2208O
1209N
2209O
1210N
2210O

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 841 - 84
21METMETVALVALBB1 - 841 - 84
12METMETVALVALAA1 - 841 - 84
22METMETVALVALCC1 - 841 - 84
13METMETVALVALAA1 - 841 - 84
23METMETVALVALDD1 - 841 - 84
14METMETVALVALAA1 - 841 - 84
24METMETVALVALEE1 - 841 - 84
15METMETVALVALAA1 - 841 - 84
25METMETVALVALFF1 - 841 - 84
16METMETVALVALAA1 - 841 - 84
26METMETVALVALGG1 - 841 - 84
17METMETVALVALAA1 - 841 - 84
27METMETVALVALHH1 - 841 - 84
18METMETVALVALAA1 - 841 - 84
28METMETVALVALII1 - 841 - 84
19METMETVALVALAA1 - 841 - 84
29METMETVALVALJJ1 - 841 - 84
110METMETVALVALAA1 - 841 - 84
210METMETVALVALKK1 - 841 - 84
111METMETVALVALAA1 - 841 - 84
211METMETVALVALLL1 - 841 - 84
112METMETVALVALAA1 - 841 - 84
212METMETVALVALMM1 - 841 - 84
113METMETVALVALAA1 - 841 - 84
213METMETVALVALNN1 - 841 - 84
114METMETVALVALAA1 - 841 - 84
214METMETVALVALOO1 - 841 - 84
115VALVALSERSERAA86 - 21986 - 219
215VALVALSERSERBB86 - 21986 - 219
116VALVALILEILEAA86 - 22086 - 220
216VALVALILEILECC86 - 22086 - 220
117VALVALTHRTHRAA86 - 21886 - 218
217VALVALTHRTHRDD86 - 21886 - 218
118VALVALSERSERAA86 - 21986 - 219
218VALVALSERSEREE86 - 21986 - 219
119VALVALSERSERAA86 - 21986 - 219
219VALVALSERSERFF86 - 21986 - 219
120VALVALSERSERAA86 - 21986 - 219
220VALVALSERSERGG86 - 21986 - 219
121VALVALSERSERAA86 - 21986 - 219
221VALVALSERSERHH86 - 21986 - 219
122VALVALILEILEAA86 - 22086 - 220
222VALVALILEILEII86 - 22086 - 220
123VALVALILEILEAA86 - 22086 - 220
223VALVALILEILEJJ86 - 22086 - 220
124VALVALILEILEAA86 - 22086 - 220
224VALVALILEILEKK86 - 22086 - 220
125VALVALILEILEAA86 - 22086 - 220
225VALVALILEILELL86 - 22086 - 220
126VALVALSERSERAA86 - 21986 - 219
226VALVALSERSERMM86 - 21986 - 219
127VALVALSERSERAA86 - 21986 - 219
227VALVALSERSERNN86 - 21986 - 219
128VALVALSERSERAA86 - 21986 - 219
228VALVALSERSEROO86 - 21986 - 219
129METMETVALVALBB1 - 841 - 84
229METMETVALVALCC1 - 841 - 84
130METMETVALVALBB1 - 841 - 84
230METMETVALVALDD1 - 841 - 84
131METMETVALVALBB1 - 841 - 84
231METMETVALVALEE1 - 841 - 84
132METMETVALVALBB1 - 841 - 84
232METMETVALVALFF1 - 841 - 84
133METMETVALVALBB1 - 841 - 84
233METMETVALVALGG1 - 841 - 84
134METMETVALVALBB1 - 841 - 84
234METMETVALVALHH1 - 841 - 84
135METMETVALVALBB1 - 841 - 84
235METMETVALVALII1 - 841 - 84
136METMETVALVALBB1 - 841 - 84
236METMETVALVALJJ1 - 841 - 84
137METMETVALVALBB1 - 841 - 84
237METMETVALVALKK1 - 841 - 84
138METMETVALVALBB1 - 841 - 84
238METMETVALVALLL1 - 841 - 84
139METMETVALVALBB1 - 841 - 84
239METMETVALVALMM1 - 841 - 84
140METMETVALVALBB1 - 841 - 84
240METMETVALVALNN1 - 841 - 84
141METMETVALVALBB1 - 841 - 84
241METMETVALVALOO1 - 841 - 84
142VALVALSERSERBB86 - 21986 - 219
242VALVALSERSERCC86 - 21986 - 219
143VALVALTHRTHRBB86 - 21886 - 218
243VALVALTHRTHRDD86 - 21886 - 218
144VALVALTHRTHRBB86 - 22186 - 221
244VALVALTHRTHREE86 - 22186 - 221
145VALVALTHRTHRBB86 - 22186 - 221
245VALVALTHRTHRFF86 - 22186 - 221
146VALVALTHRTHRBB86 - 22186 - 221
246VALVALTHRTHRGG86 - 22186 - 221
147VALVALTHRTHRBB86 - 22186 - 221
247VALVALTHRTHRHH86 - 22186 - 221
148VALVALSERSERBB86 - 21986 - 219
248VALVALSERSERII86 - 21986 - 219
149VALVALSERSERBB86 - 21986 - 219
249VALVALSERSERJJ86 - 21986 - 219
150VALVALSERSERBB86 - 21986 - 219
250VALVALSERSERKK86 - 21986 - 219
151VALVALSERSERBB86 - 21986 - 219
251VALVALSERSERLL86 - 21986 - 219
152VALVALTHRTHRBB86 - 22186 - 221
252VALVALTHRTHRMM86 - 22186 - 221
153VALVALTHRTHRBB86 - 22186 - 221
253VALVALTHRTHRNN86 - 22186 - 221
154VALVALTHRTHRBB86 - 22186 - 221
254VALVALTHRTHROO86 - 22186 - 221
155METMETVALVALCC1 - 841 - 84
255METMETVALVALDD1 - 841 - 84
156METMETVALVALCC1 - 841 - 84
256METMETVALVALEE1 - 841 - 84
157METMETVALVALCC1 - 841 - 84
257METMETVALVALFF1 - 841 - 84
158METMETVALVALCC1 - 841 - 84
258METMETVALVALGG1 - 841 - 84
159METMETVALVALCC1 - 841 - 84
259METMETVALVALHH1 - 841 - 84
160METMETVALVALCC1 - 841 - 84
260METMETVALVALII1 - 841 - 84
161METMETVALVALCC1 - 841 - 84
261METMETVALVALJJ1 - 841 - 84
162METMETVALVALCC1 - 841 - 84
262METMETVALVALKK1 - 841 - 84
163METMETVALVALCC1 - 841 - 84
263METMETVALVALLL1 - 841 - 84
164METMETVALVALCC1 - 841 - 84
264METMETVALVALMM1 - 841 - 84
165METMETVALVALCC1 - 841 - 84
265METMETVALVALNN1 - 841 - 84
166METMETVALVALCC1 - 841 - 84
266METMETVALVALOO1 - 841 - 84
167VALVALTHRTHRCC86 - 21886 - 218
267VALVALTHRTHRDD86 - 21886 - 218
168VALVALSERSERCC86 - 21986 - 219
268VALVALSERSEREE86 - 21986 - 219
169VALVALSERSERCC86 - 21986 - 219
269VALVALSERSERFF86 - 21986 - 219
170VALVALSERSERCC86 - 21986 - 219
270VALVALSERSERGG86 - 21986 - 219
171VALVALSERSERCC86 - 21986 - 219
271VALVALSERSERHH86 - 21986 - 219
172VALVALILEILECC86 - 22086 - 220
272VALVALILEILEII86 - 22086 - 220
173VALVALILEILECC86 - 22086 - 220
273VALVALILEILEJJ86 - 22086 - 220
174VALVALILEILECC86 - 22086 - 220
274VALVALILEILEKK86 - 22086 - 220
175VALVALILEILECC86 - 22086 - 220
275VALVALILEILELL86 - 22086 - 220
176VALVALSERSERCC86 - 21986 - 219
276VALVALSERSERMM86 - 21986 - 219
177VALVALSERSERCC86 - 21986 - 219
277VALVALSERSERNN86 - 21986 - 219
178VALVALSERSERCC86 - 21986 - 219
278VALVALSERSEROO86 - 21986 - 219
179METMETVALVALDD1 - 841 - 84
279METMETVALVALEE1 - 841 - 84
180METMETVALVALDD1 - 841 - 84
280METMETVALVALFF1 - 841 - 84
181METMETVALVALDD1 - 841 - 84
281METMETVALVALGG1 - 841 - 84
182METMETVALVALDD1 - 841 - 84
282METMETVALVALHH1 - 841 - 84
183METMETVALVALDD1 - 841 - 84
283METMETVALVALII1 - 841 - 84
184METMETVALVALDD1 - 841 - 84
284METMETVALVALJJ1 - 841 - 84
185METMETVALVALDD1 - 841 - 84
285METMETVALVALKK1 - 841 - 84
186METMETVALVALDD1 - 841 - 84
286METMETVALVALLL1 - 841 - 84
187METMETVALVALDD1 - 841 - 84
287METMETVALVALMM1 - 841 - 84
188METMETVALVALDD1 - 841 - 84
288METMETVALVALNN1 - 841 - 84
189METMETVALVALDD1 - 841 - 84
289METMETVALVALOO1 - 841 - 84
190VALVALTHRTHRDD86 - 21886 - 218
290VALVALTHRTHREE86 - 21886 - 218
191VALVALTHRTHRDD86 - 21886 - 218
291VALVALTHRTHRFF86 - 21886 - 218
192VALVALTHRTHRDD86 - 21886 - 218
292VALVALTHRTHRGG86 - 21886 - 218
193VALVALTHRTHRDD86 - 21886 - 218
293VALVALTHRTHRHH86 - 21886 - 218
194VALVALTHRTHRDD86 - 21886 - 218
294VALVALTHRTHRII86 - 21886 - 218
195VALVALTHRTHRDD86 - 21886 - 218
295VALVALTHRTHRJJ86 - 21886 - 218
196VALVALTHRTHRDD86 - 21886 - 218
296VALVALTHRTHRKK86 - 21886 - 218
197VALVALTHRTHRDD86 - 21886 - 218
297VALVALTHRTHRLL86 - 21886 - 218
198VALVALTHRTHRDD86 - 21886 - 218
298VALVALTHRTHRMM86 - 21886 - 218
199VALVALTHRTHRDD86 - 21886 - 218
299VALVALTHRTHRNN86 - 21886 - 218
1100VALVALTHRTHRDD86 - 21886 - 218
2100VALVALTHRTHROO86 - 21886 - 218
1101METMETVALVALEE1 - 841 - 84
2101METMETVALVALFF1 - 841 - 84
1102METMETVALVALEE1 - 841 - 84
2102METMETVALVALGG1 - 841 - 84
1103METMETVALVALEE1 - 841 - 84
2103METMETVALVALHH1 - 841 - 84
1104METMETVALVALEE1 - 841 - 84
2104METMETVALVALII1 - 841 - 84
1105METMETVALVALEE1 - 841 - 84
2105METMETVALVALJJ1 - 841 - 84
1106METMETVALVALEE1 - 841 - 84
2106METMETVALVALKK1 - 841 - 84
1107METMETVALVALEE1 - 841 - 84
2107METMETVALVALLL1 - 841 - 84
1108METMETVALVALEE1 - 841 - 84
2108METMETVALVALMM1 - 841 - 84
1109METMETVALVALEE1 - 841 - 84
2109METMETVALVALNN1 - 841 - 84
1110METMETVALVALEE1 - 841 - 84
2110METMETVALVALOO1 - 841 - 84
1111VALVALTHRTHREE86 - 22186 - 221
2111VALVALTHRTHRFF86 - 22186 - 221
1112VALVALTHRTHREE86 - 22186 - 221
2112VALVALTHRTHRGG86 - 22186 - 221
1113VALVALTHRTHREE86 - 22186 - 221
2113VALVALTHRTHRHH86 - 22186 - 221
1114VALVALSERSEREE86 - 21986 - 219
2114VALVALSERSERII86 - 21986 - 219
1115VALVALSERSEREE86 - 21986 - 219
2115VALVALSERSERJJ86 - 21986 - 219
1116VALVALSERSEREE86 - 21986 - 219
2116VALVALSERSERKK86 - 21986 - 219
1117VALVALSERSEREE86 - 21986 - 219
2117VALVALSERSERLL86 - 21986 - 219
1118VALVALTHRTHREE86 - 22186 - 221
2118VALVALTHRTHRMM86 - 22186 - 221
1119VALVALTHRTHREE86 - 22186 - 221
2119VALVALTHRTHRNN86 - 22186 - 221
1120VALVALTHRTHREE86 - 22186 - 221
2120VALVALTHRTHROO86 - 22186 - 221
1121METMETVALVALFF1 - 841 - 84
2121METMETVALVALGG1 - 841 - 84
1122METMETVALVALFF1 - 841 - 84
2122METMETVALVALHH1 - 841 - 84
1123METMETVALVALFF1 - 841 - 84
2123METMETVALVALII1 - 841 - 84
1124METMETVALVALFF1 - 841 - 84
2124METMETVALVALJJ1 - 841 - 84
1125METMETVALVALFF1 - 841 - 84
2125METMETVALVALKK1 - 841 - 84
1126METMETVALVALFF1 - 841 - 84
2126METMETVALVALLL1 - 841 - 84
1127METMETVALVALFF1 - 841 - 84
2127METMETVALVALMM1 - 841 - 84
1128METMETVALVALFF1 - 841 - 84
2128METMETVALVALNN1 - 841 - 84
1129METMETVALVALFF1 - 841 - 84
2129METMETVALVALOO1 - 841 - 84
1130VALVALTHRTHRFF86 - 22186 - 221
2130VALVALTHRTHRGG86 - 22186 - 221
1131VALVALTHRTHRFF86 - 22186 - 221
2131VALVALTHRTHRHH86 - 22186 - 221
1132VALVALSERSERFF86 - 21986 - 219
2132VALVALSERSERII86 - 21986 - 219
1133VALVALSERSERFF86 - 21986 - 219
2133VALVALSERSERJJ86 - 21986 - 219
1134VALVALSERSERFF86 - 21986 - 219
2134VALVALSERSERKK86 - 21986 - 219
1135VALVALSERSERFF86 - 21986 - 219
2135VALVALSERSERLL86 - 21986 - 219
1136VALVALTHRTHRFF86 - 22186 - 221
2136VALVALTHRTHRMM86 - 22186 - 221
1137VALVALTHRTHRFF86 - 22186 - 221
2137VALVALTHRTHRNN86 - 22186 - 221
1138VALVALTHRTHRFF86 - 22186 - 221
2138VALVALTHRTHROO86 - 22186 - 221
1139METMETVALVALGG1 - 841 - 84
2139METMETVALVALHH1 - 841 - 84
1140METMETVALVALGG1 - 841 - 84
2140METMETVALVALII1 - 841 - 84
1141METMETVALVALGG1 - 841 - 84
2141METMETVALVALJJ1 - 841 - 84
1142METMETVALVALGG1 - 841 - 84
2142METMETVALVALKK1 - 841 - 84
1143METMETVALVALGG1 - 841 - 84
2143METMETVALVALLL1 - 841 - 84
1144METMETVALVALGG1 - 841 - 84
2144METMETVALVALMM1 - 841 - 84
1145METMETVALVALGG1 - 841 - 84
2145METMETVALVALNN1 - 841 - 84
1146METMETVALVALGG1 - 841 - 84
2146METMETVALVALOO1 - 841 - 84
1147VALVALTHRTHRGG86 - 22186 - 221
2147VALVALTHRTHRHH86 - 22186 - 221
1148VALVALSERSERGG86 - 21986 - 219
2148VALVALSERSERII86 - 21986 - 219
1149VALVALSERSERGG86 - 21986 - 219
2149VALVALSERSERJJ86 - 21986 - 219
1150VALVALSERSERGG86 - 21986 - 219
2150VALVALSERSERKK86 - 21986 - 219
1151VALVALSERSERGG86 - 21986 - 219
2151VALVALSERSERLL86 - 21986 - 219
1152VALVALTHRTHRGG86 - 22186 - 221
2152VALVALTHRTHRMM86 - 22186 - 221
1153VALVALTHRTHRGG86 - 22186 - 221
2153VALVALTHRTHRNN86 - 22186 - 221
1154VALVALTHRTHRGG86 - 22186 - 221
2154VALVALTHRTHROO86 - 22186 - 221
1155METMETVALVALHH1 - 841 - 84
2155METMETVALVALII1 - 841 - 84
1156METMETVALVALHH1 - 841 - 84
2156METMETVALVALJJ1 - 841 - 84
1157METMETVALVALHH1 - 841 - 84
2157METMETVALVALKK1 - 841 - 84
1158METMETVALVALHH1 - 841 - 84
2158METMETVALVALLL1 - 841 - 84
1159METMETVALVALHH1 - 841 - 84
2159METMETVALVALMM1 - 841 - 84
1160METMETVALVALHH1 - 841 - 84
2160METMETVALVALNN1 - 841 - 84
1161METMETVALVALHH1 - 841 - 84
2161METMETVALVALOO1 - 841 - 84
1162VALVALSERSERHH86 - 21986 - 219
2162VALVALSERSERII86 - 21986 - 219
1163VALVALSERSERHH86 - 21986 - 219
2163VALVALSERSERJJ86 - 21986 - 219
1164VALVALSERSERHH86 - 21986 - 219
2164VALVALSERSERKK86 - 21986 - 219
1165VALVALSERSERHH86 - 21986 - 219
2165VALVALSERSERLL86 - 21986 - 219
1166VALVALTHRTHRHH86 - 22186 - 221
2166VALVALTHRTHRMM86 - 22186 - 221
1167VALVALTHRTHRHH86 - 22186 - 221
2167VALVALTHRTHRNN86 - 22186 - 221
1168VALVALTHRTHRHH86 - 22186 - 221
2168VALVALTHRTHROO86 - 22186 - 221
1169METMETVALVALII1 - 841 - 84
2169METMETVALVALJJ1 - 841 - 84
1170METMETVALVALII1 - 841 - 84
2170METMETVALVALKK1 - 841 - 84
1171METMETVALVALII1 - 841 - 84
2171METMETVALVALLL1 - 841 - 84
1172METMETVALVALII1 - 841 - 84
2172METMETVALVALMM1 - 841 - 84
1173METMETVALVALII1 - 841 - 84
2173METMETVALVALNN1 - 841 - 84
1174METMETVALVALII1 - 841 - 84
2174METMETVALVALOO1 - 841 - 84
1175VALVALILEILEII86 - 22086 - 220
2175VALVALILEILEJJ86 - 22086 - 220
1176VALVALILEILEII86 - 22086 - 220
2176VALVALILEILEKK86 - 22086 - 220
1177VALVALILEILEII86 - 22086 - 220
2177VALVALILEILELL86 - 22086 - 220
1178VALVALSERSERII86 - 21986 - 219
2178VALVALSERSERMM86 - 21986 - 219
1179VALVALSERSERII86 - 21986 - 219
2179VALVALSERSERNN86 - 21986 - 219
1180VALVALSERSERII86 - 21986 - 219
2180VALVALSERSEROO86 - 21986 - 219
1181METMETVALVALJJ1 - 841 - 84
2181METMETVALVALKK1 - 841 - 84
1182METMETVALVALJJ1 - 841 - 84
2182METMETVALVALLL1 - 841 - 84
1183METMETVALVALJJ1 - 841 - 84
2183METMETVALVALMM1 - 841 - 84
1184METMETVALVALJJ1 - 841 - 84
2184METMETVALVALNN1 - 841 - 84
1185METMETVALVALJJ1 - 841 - 84
2185METMETVALVALOO1 - 841 - 84
1186VALVALILEILEJJ86 - 22086 - 220
2186VALVALILEILEKK86 - 22086 - 220
1187VALVALILEILEJJ86 - 22086 - 220
2187VALVALILEILELL86 - 22086 - 220
1188VALVALSERSERJJ86 - 21986 - 219
2188VALVALSERSERMM86 - 21986 - 219
1189VALVALSERSERJJ86 - 21986 - 219
2189VALVALSERSERNN86 - 21986 - 219
1190VALVALSERSERJJ86 - 21986 - 219
2190VALVALSERSEROO86 - 21986 - 219
1191METMETVALVALKK1 - 841 - 84
2191METMETVALVALLL1 - 841 - 84
1192METMETVALVALKK1 - 841 - 84
2192METMETVALVALMM1 - 841 - 84
1193METMETVALVALKK1 - 841 - 84
2193METMETVALVALNN1 - 841 - 84
1194METMETVALVALKK1 - 841 - 84
2194METMETVALVALOO1 - 841 - 84
1195VALVALILEILEKK86 - 22086 - 220
2195VALVALILEILELL86 - 22086 - 220
1196VALVALSERSERKK86 - 21986 - 219
2196VALVALSERSERMM86 - 21986 - 219
1197VALVALSERSERKK86 - 21986 - 219
2197VALVALSERSERNN86 - 21986 - 219
1198VALVALSERSERKK86 - 21986 - 219
2198VALVALSERSEROO86 - 21986 - 219
1199METMETVALVALLL1 - 841 - 84
2199METMETVALVALMM1 - 841 - 84
1200METMETVALVALLL1 - 841 - 84
2200METMETVALVALNN1 - 841 - 84
1201METMETVALVALLL1 - 841 - 84
2201METMETVALVALOO1 - 841 - 84
1202VALVALSERSERLL86 - 21986 - 219
2202VALVALSERSERMM86 - 21986 - 219
1203VALVALSERSERLL86 - 21986 - 219
2203VALVALSERSERNN86 - 21986 - 219
1204VALVALSERSERLL86 - 21986 - 219
2204VALVALSERSEROO86 - 21986 - 219
1205METMETVALVALMM1 - 841 - 84
2205METMETVALVALNN1 - 841 - 84
1206METMETVALVALMM1 - 841 - 84
2206METMETVALVALOO1 - 841 - 84
1207VALVALTHRTHRMM86 - 22186 - 221
2207VALVALTHRTHRNN86 - 22186 - 221
1208VALVALTHRTHRMM86 - 22186 - 221
2208VALVALTHRTHROO86 - 22186 - 221
1209METMETVALVALNN1 - 841 - 84
2209METMETVALVALOO1 - 841 - 84
1210VALVALTHRTHRNN86 - 22186 - 221
2210VALVALTHRTHROO86 - 22186 - 221

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
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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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
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171
172
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174
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176
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180
181
182
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191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210

-
Components

#1: Protein
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA


Mass: 23938.730 Da / Num. of mol.: 15 / Mutation: R134V, S166G
Source method: isolated from a genetically manipulated source
Details: contains C-terminal His-tag lysine 85 is covalently modified
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fsaA, fsa, mipB, ybiZ, b0825, JW5109 / Plasmid: pGT7-FSA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2-1.6 M ammonium sulfate, 50-150 mM NaCl, 100 mM Tris or Bicine pH 8.5-8.75
PH range: 8.5-8.75

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.62→49.7 Å / Num. obs: 112831 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.3 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.077 / Rrim(I) all: 0.144 / Net I/σ(I): 7.2
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1 / Num. unique obs: 10827 / CC1/2: 0.65 / Rpim(I) all: 0.575 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1l6w
Resolution: 2.62→49.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 20.017 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.97 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 5735 5.1 %RANDOM
Rwork0.2195 ---
obs0.2216 107028 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.86 Å2 / Biso mean: 58.979 Å2 / Biso min: 25.41 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å25.51 Å2
2---5.19 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.62→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24273 0 9291 177 33741
Biso mean--68.59 40.77 -
Num. residues----2047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01324725
X-RAY DIFFRACTIONr_bond_other_d0.0010.01724277
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.64133579
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58556261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37853280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00224.217894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.545154022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.5231575
X-RAY DIFFRACTIONr_chiral_restr0.0590.23458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0227282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024350
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23100.05
12B23100.05
21A23230.04
22C23230.04
31A23220.04
32D23220.04
41A23120.07
42E23120.07
51A23110.04
52F23110.04
61A23350.03
62G23350.03
71A23130.05
72H23130.05
81A23150.05
82I23150.05
91A23200.05
92J23200.05
101A23190.05
102K23190.05
111A23200.04
112L23200.04
121A23110.04
122M23110.04
131A23270.04
132N23270.04
141A23190.04
142O23190.04
151A38530.01
152B38530.01
161A38380.03
162C38380.03
171A38030.04
172D38030.04
181A38040.03
182E38040.03
191A38320.02
192F38320.02
201A38290.02
202G38290.02
211A38260.03
212H38260.03
221A38540.03
222I38540.03
231A38340.04
232J38340.04
241A38540.03
242K38540.03
251A38480.04
252L38480.04
261A38140.03
262M38140.03
271A38360.02
272N38360.02
281A38460.02
282O38460.02
291B23180.04
292C23180.04
301B23100.05
302D23100.05
311B23040.07
312E23040.07
321B23040.05
322F23040.05
331B23170.04
332G23170.04
341B23310.04
342H23310.04
351B23070.06
352I23070.06
361B23190.03
362J23190.03
371B23220.04
372K23220.04
381B23100.05
382L23100.05
391B22970.05
392M22970.05
401B23160.03
402N23160.03
411B23260.03
412O23260.03
421B38340.03
422C38340.03
431B38130.04
432D38130.04
441B38670.03
442E38670.03
451B39010.02
452F39010.02
461B38890.02
462G38890.02
471B38970.02
472H38970.02
481B38430.02
482I38430.02
491B38260.04
492J38260.04
501B38410.03
502K38410.03
511B38320.03
512L38320.03
521B38760.02
522M38760.02
531B39000.02
532N39000.02
541B39110
542O39110
551C23130.03
552D23130.03
561C23040.06
562E23040.06
571C23050.03
572F23050.03
581C23270.03
582G23270.03
591C23220.04
592H23220.04
601C23120.05
602I23120.05
611C23230.04
612J23230.04
621C23290.03
622K23290.03
631C23120.04
632L23120.04
641C23040.04
642M23040.04
651C23200.04
652N23200.04
661C23260.03
662O23260.03
671C37840.05
672D37840.05
681C37980.04
682E37980.04
691C38170.03
692F38170.03
701C38110.03
702G38110.03
711C38180.03
712H38180.03
721C38630.02
722I38630.02
731C38490.03
732J38490.03
741C38430.03
742K38430.03
751C38370.04
752L38370.04
761C38090.03
762M38090.03
771C38210.03
772N38210.03
781C38220.03
782O38220.03
791D23180.06
792E23180.06
801D23170.04
802F23170.04
811D23270.03
812G23270.03
821D23230.04
822H23230.04
831D23210.05
832I23210.05
841D23190.04
842J23190.04
851D23260.04
852K23260.04
861D23290.04
862L23290.04
871D23120.04
872M23120.04
881D23230.03
882N23230.03
891D23190.04
892O23190.04
901D38240.05
902E38240.05
911D38600.04
912F38600.04
921D38390.05
922G38390.05
931D38520.04
932H38520.04
941D38440.05
942I38440.05
951D38480.04
952J38480.04
961D38420.04
962K38420.04
971D38580.04
972L38580.04
981D38320.04
982M38320.04
991D38480.04
992N38480.04
1001D38680.04
1002O38680.04
1011E23420.06
1012F23420.06
1021E23230.06
1022G23230.06
1031E23060.07
1032H23060.07
1041E23100.07
1042I23100.07
1051E23020.07
1052J23020.07
1061E23090.07
1062K23090.07
1071E23160.06
1072L23160.06
1081E23500.06
1082M23500.06
1091E23060.06
1092N23060.06
1101E23010.06
1102O23010.06
1111E38830.04
1112F38830.04
1121E38950.03
1122G38950.03
1131E38810.04
1132H38810.04
1141E38310.04
1142I38310.04
1151E38200.04
1152J38200.04
1161E38160.05
1162K38160.05
1171E38440.04
1172L38440.04
1181E39270.02
1182M39270.02
1191E38890.04
1192N38890.04
1201E38900.03
1202O38900.03
1211F23180.03
1212G23180.03
1221F23110.04
1222H23110.04
1231F23130.04
1232I23130.04
1241F23050.04
1242J23050.04
1251F23150.03
1252K23150.03
1261F23230.02
1262L23230.02
1271F23360.03
1272M23360.03
1281F23060.04
1282N23060.04
1291F23010.04
1292O23010.04
1301F38980.03
1302G38980.03
1311F39060.03
1312H39060.03
1321F38500.03
1322I38500.03
1331F38450.04
1332J38450.04
1341F38470.04
1342K38470.04
1351F38510.04
1352L38510.04
1361F38920.03
1362M38920.03
1371F39020.03
1372N39020.03
1381F39240.02
1382O39240.02
1391G23200.04
1392H23200.04
1401G23230.05
1402I23230.05
1411G23260.04
1412J23260.04
1421G23220.03
1422K23220.03
1431G23250.02
1432L23250.02
1441G23150.04
1442M23150.04
1451G23320.03
1452N23320.03
1461G23260.03
1462O23260.03
1471G38930.03
1472H38930.03
1481G38540.03
1482I38540.03
1491G38420.04
1492J38420.04
1501G38380.04
1502K38380.04
1511G38620.03
1512L38620.03
1521G38870.03
1522M38870.03
1531G39130.03
1532N39130.03
1541G39020.03
1542O39020.03
1551H23160.05
1552I23160.05
1561H23290.01
1562J23290.01
1571H23300.03
1572K23300.03
1581H23190.04
1582L23190.04
1591H22990.05
1592M22990.05
1601H23200.03
1602N23200.03
1611H23280.03
1612O23280.03
1621H38220.03
1622I38220.03
1631H38090.04
1632J38090.04
1641H38080.04
1642K38080.04
1651H38160.04
1652L38160.04
1661H38570.03
1662M38570.03
1671H38740.03
1672N38740.03
1681H38870.02
1682O38870.02
1691I23090.05
1692J23090.05
1701I23270.05
1702K23270.05
1711I23210.04
1712L23210.04
1721I23030.05
1722M23030.05
1731I23110.05
1732N23110.05
1741I23090.05
1742O23090.05
1751I38510.04
1752J38510.04
1761I38570.03
1762K38570.03
1771I38460.04
1772L38460.04
1781I38090.03
1782M38090.03
1791I38290.03
1792N38290.03
1801I38250.03
1802O38250.03
1811J23260.03
1812K23260.03
1821J23180.04
1822L23180.04
1831J22980.05
1832M22980.05
1841J23230.03
1842N23230.03
1851J23310.03
1852O23310.03
1861J38320.04
1862K38320.04
1871J38510.04
1872L38510.04
1881J38010.04
1882M38010.04
1891J38170.03
1892N38170.03
1901J38210.04
1902O38210.04
1911K23260.02
1912L23260.02
1921K23040.04
1922M23040.04
1931K23160.04
1932N23160.04
1941K23290.04
1942O23290.04
1951K38290.04
1952L38290.04
1961K37920.04
1962M37920.04
1971K38150.03
1972N38150.03
1981K38240.03
1982O38240.03
1991L23120.03
1992M23120.03
2001L23130.04
2002N23130.04
2011L23090.04
2012O23090.04
2021L38350.04
2022M38350.04
2031L38490.03
2032N38490.03
2041L38500.03
2042O38500.03
2051M23040.04
2052N23040.04
2061M22970.04
2062O22970.04
2071M38620.03
2072N38620.03
2081M38650.02
2082O38650.02
2091N23240.03
2092O23240.03
2101N39120.04
2102O39120.04
LS refinement shellResolution: 2.62→2.688 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 409 -
Rwork0.437 7673 -
all-8082 -
obs--95.99 %

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