[English] 日本語
Yorodumi
- PDB-6koi: Crystal structure of SNX11-PXe domain in dimer form. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6koi
TitleCrystal structure of SNX11-PXe domain in dimer form.
ComponentsSorting nexin-11
KeywordsPROTEIN TRANSPORT / sorting nexin / phox-homology domain
Function / homology
Function and homology information


phosphatidylinositol phosphate binding / vesicle organization / intracellular protein transport / endosome / membrane
Similarity search - Function
Sorting nexin-10/11 / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsXu, T. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31570759 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Molecular Basis for PI(3,5)P2Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation.
Authors: Xu, T. / Gan, Q. / Wu, B. / Yin, M. / Xu, J. / Shu, X. / Liu, J.
History
DepositionAug 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting nexin-11
B: Sorting nexin-11
C: Sorting nexin-11
D: Sorting nexin-11
E: Sorting nexin-11
F: Sorting nexin-11
G: Sorting nexin-11
H: Sorting nexin-11
I: Sorting nexin-11
J: Sorting nexin-11
K: Sorting nexin-11
L: Sorting nexin-11
M: Sorting nexin-11
N: Sorting nexin-11
O: Sorting nexin-11
P: Sorting nexin-11
Q: Sorting nexin-11
R: Sorting nexin-11
S: Sorting nexin-11
T: Sorting nexin-11
U: Sorting nexin-11
V: Sorting nexin-11
W: Sorting nexin-11
X: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)451,96424
Polymers451,96424
Non-polymers00
Water00
1
A: Sorting nexin-11
B: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-10 kcal/mol
Surface area15090 Å2
MethodPISA
2
C: Sorting nexin-11
D: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area15790 Å2
MethodPISA
3
E: Sorting nexin-11
F: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-11 kcal/mol
Surface area15210 Å2
MethodPISA
4
G: Sorting nexin-11
H: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-12 kcal/mol
Surface area15830 Å2
MethodPISA
5
I: Sorting nexin-11
J: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-10 kcal/mol
Surface area15330 Å2
MethodPISA
6
K: Sorting nexin-11
L: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9 kcal/mol
Surface area15300 Å2
MethodPISA
7
M: Sorting nexin-11
N: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 kcal/mol
Surface area15390 Å2
MethodPISA
8
O: Sorting nexin-11
P: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-11 kcal/mol
Surface area14910 Å2
MethodPISA
9
Q: Sorting nexin-11
R: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area15020 Å2
MethodPISA
10
S: Sorting nexin-11
T: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-11 kcal/mol
Surface area15470 Å2
MethodPISA
11
U: Sorting nexin-11
V: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8 kcal/mol
Surface area14980 Å2
MethodPISA
12
W: Sorting nexin-11
X: Sorting nexin-11


Theoretical massNumber of molelcules
Total (without water)37,6642
Polymers37,6642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.040, 190.434, 237.012
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
118A
218S
119A
219T
120A
220U
121A
221V
122A
222W
123A
223X
124B
224C
125B
225D
126B
226E
127B
227F
128B
228G
129B
229H
130B
230I
131B
231J
132B
232K
133B
233L
134B
234M
135B
235N
136B
236O
137B
237P
138B
238Q
139B
239R
140B
240S
141B
241T
142B
242U
143B
243V
144B
244W
145B
245X
146C
246D
147C
247E
148C
248F
149C
249G
150C
250H
151C
251I
152C
252J
153C
253K
154C
254L
155C
255M
156C
256N
157C
257O
158C
258P
159C
259Q
160C
260R
161C
261S
162C
262T
163C
263U
164C
264V
165C
265W
166C
266X
167D
267E
168D
268F
169D
269G
170D
270H
171D
271I
172D
272J
173D
273K
174D
274L
175D
275M
176D
276N
177D
277O
178D
278P
179D
279Q
180D
280R
181D
281S
182D
282T
183D
283U
184D
284V
185D
285W
186D
286X
187E
287F
188E
288G
189E
289H
190E
290I
191E
291J
192E
292K
193E
293L
194E
294M
195E
295N
196E
296O
197E
297P
198E
298Q
199E
299R
1100E
2100S
1101E
2101T
1102E
2102U
1103E
2103V
1104E
2104W
1105E
2105X
1106F
2106G
1107F
2107H
1108F
2108I
1109F
2109J
1110F
2110K
1111F
2111L
1112F
2112M
1113F
2113N
1114F
2114O
1115F
2115P
1116F
2116Q
1117F
2117R
1118F
2118S
1119F
2119T
1120F
2120U
1121F
2121V
1122F
2122W
1123F
2123X
1124G
2124H
1125G
2125I
1126G
2126J
1127G
2127K
1128G
2128L
1129G
2129M
1130G
2130N
1131G
2131O
1132G
2132P
1133G
2133Q
1134G
2134R
1135G
2135S
1136G
2136T
1137G
2137U
1138G
2138V
1139G
2139W
1140G
2140X
1141H
2141I
1142H
2142J
1143H
2143K
1144H
2144L
1145H
2145M
1146H
2146N
1147H
2147O
1148H
2148P
1149H
2149Q
1150H
2150R
1151H
2151S
1152H
2152T
1153H
2153U
1154H
2154V
1155H
2155W
1156H
2156X
1157I
2157J
1158I
2158K
1159I
2159L
1160I
2160M
1161I
2161N
1162I
2162O
1163I
2163P
1164I
2164Q
1165I
2165R
1166I
2166S
1167I
2167T
1168I
2168U
1169I
2169V
1170I
2170W
1171I
2171X
1172J
2172K
1173J
2173L
1174J
2174M
1175J
2175N
1176J
2176O
1177J
2177P
1178J
2178Q
1179J
2179R
1180J
2180S
1181J
2181T
1182J
2182U
1183J
2183V
1184J
2184W
1185J
2185X
1186K
2186L
1187K
2187M
1188K
2188N
1189K
2189O
1190K
2190P
1191K
2191Q
1192K
2192R
1193K
2193S
1194K
2194T
1195K
2195U
1196K
2196V
1197K
2197W
1198K
2198X
1199L
2199M
1200L
2200N
1201L
2201O
1202L
2202P
1203L
2203Q
1204L
2204R
1205L
2205S
1206L
2206T
1207L
2207U
1208L
2208V
1209L
2209W
1210L
2210X
1211M
2211N
1212M
2212O
1213M
2213P
1214M
2214Q
1215M
2215R
1216M
2216S
1217M
2217T
1218M
2218U
1219M
2219V
1220M
2220W
1221M
2221X
1222N
2222O
1223N
2223P
1224N
2224Q
1225N
2225R
1226N
2226S
1227N
2227T
1228N
2228U
1229N
2229V
1230N
2230W
1231N
2231X
1232O
2232P
1233O
2233Q
1234O
2234R
1235O
2235S
1236O
2236T
1237O
2237U
1238O
2238V
1239O
2239W
1240O
2240X
1241P
2241Q
1242P
2242R
1243P
2243S
1244P
2244T
1245P
2245U
1246P
2246V
1247P
2247W
1248P
2248X
1249Q
2249R
1250Q
2250S
1251Q
2251T
1252Q
2252U
1253Q
2253V
1254Q
2254W
1255Q
2255X
1256R
2256S
1257R
2257T
1258R
2258U
1259R
2259V
1260R
2260W
1261R
2261X
1262S
2262T
1263S
2263U
1264S
2264V
1265S
2265W
1266S
2266X
1267T
2267U
1268T
2268V
1269T
2269W
1270T
2270X
1271U
2271V
1272U
2272W
1273U
2273X
1274V
2274W
1275V
2275X
1276W
2276X

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
11VALVALCYSCYSAA16 - 13810 - 132
21VALVALCYSCYSBB16 - 13810 - 132
12VALVALCYSCYSAA16 - 13810 - 132
22VALVALCYSCYSCC16 - 13810 - 132
13VALVALCYSCYSAA16 - 13810 - 132
23VALVALCYSCYSDD16 - 13810 - 132
14VALVALCYSCYSAA16 - 13810 - 132
24VALVALCYSCYSEE16 - 13810 - 132
15ILEILECYSCYSAA17 - 13811 - 132
25ILEILECYSCYSFF17 - 13811 - 132
16VALVALCYSCYSAA16 - 13810 - 132
26VALVALCYSCYSGG16 - 13810 - 132
17VALVALCYSCYSAA16 - 13810 - 132
27VALVALCYSCYSHH16 - 13810 - 132
18VALVALCYSCYSAA16 - 13810 - 132
28VALVALCYSCYSII16 - 13810 - 132
19VALVALCYSCYSAA16 - 13810 - 132
29VALVALCYSCYSJJ16 - 13810 - 132
110VALVALVALVALAA16 - 13910 - 133
210VALVALVALVALKK16 - 13910 - 133
111VALVALCYSCYSAA16 - 13810 - 132
211VALVALCYSCYSLL16 - 13810 - 132
112VALVALCYSCYSAA16 - 13810 - 132
212VALVALCYSCYSMM16 - 13810 - 132
113VALVALCYSCYSAA16 - 13810 - 132
213VALVALCYSCYSNN16 - 13810 - 132
114VALVALVALVALAA16 - 13910 - 133
214VALVALVALVALOO16 - 13910 - 133
115VALVALCYSCYSAA16 - 13810 - 132
215VALVALCYSCYSPP16 - 13810 - 132
116VALVALVALVALAA16 - 13910 - 133
216VALVALVALVALQQ16 - 13910 - 133
117VALVALCYSCYSAA16 - 13810 - 132
217VALVALCYSCYSRR16 - 13810 - 132
118VALVALVALVALAA16 - 13910 - 133
218VALVALVALVALSS16 - 13910 - 133
119VALVALCYSCYSAA16 - 13810 - 132
219VALVALCYSCYSTT16 - 13810 - 132
120VALVALVALVALAA16 - 13910 - 133
220VALVALVALVALUU16 - 13910 - 133
121ILEILECYSCYSAA17 - 13811 - 132
221ILEILECYSCYSVV17 - 13811 - 132
122VALVALVALVALAA16 - 13910 - 133
222VALVALVALVALWW16 - 13910 - 133
123VALVALCYSCYSAA16 - 13810 - 132
223VALVALCYSCYSXX16 - 13810 - 132
124GLUGLUVALVALBB15 - 1399 - 133
224GLUGLUVALVALCC15 - 1399 - 133
125GLUGLUGLUGLUBB15 - 1609 - 154
225GLUGLUGLUGLUDD15 - 1609 - 154
126VALVALVALVALBB16 - 13910 - 133
226VALVALVALVALEE16 - 13910 - 133
127ILEILELEULEUBB17 - 15911 - 153
227ILEILELEULEUFF17 - 15911 - 153
128GLUGLUVALVALBB15 - 1399 - 133
228GLUGLUVALVALGG15 - 1399 - 133
129GLUGLUGLUGLUBB15 - 1609 - 154
229GLUGLUGLUGLUHH15 - 1609 - 154
130GLUGLUCYSCYSBB15 - 1389 - 132
230GLUGLUCYSCYSII15 - 1389 - 132
131GLUGLULEULEUBB15 - 1599 - 153
231GLUGLULEULEUJJ15 - 1599 - 153
132VALVALVALVALBB16 - 13910 - 133
232VALVALVALVALKK16 - 13910 - 133
133GLUGLUGLUGLUBB15 - 1609 - 154
233GLUGLUGLUGLULL15 - 1609 - 154
134VALVALVALVALBB16 - 13910 - 133
234VALVALVALVALMM16 - 13910 - 133
135GLUGLUASNASNBB15 - 1589 - 152
235GLUGLUASNASNNN15 - 1589 - 152
136VALVALCYSCYSBB16 - 13810 - 132
236VALVALCYSCYSOO16 - 13810 - 132
137GLUGLULEULEUBB15 - 1599 - 153
237GLUGLULEULEUPP15 - 1599 - 153
138VALVALCYSCYSBB16 - 13810 - 132
238VALVALCYSCYSQQ16 - 13810 - 132
139VALVALASNASNBB16 - 15810 - 152
239VALVALASNASNRR16 - 15810 - 152
140VALVALCYSCYSBB16 - 13810 - 132
240VALVALCYSCYSSS16 - 13810 - 132
141VALVALGLUGLUBB16 - 16010 - 154
241VALVALGLUGLUTT16 - 16010 - 154
142VALVALVALVALBB16 - 13910 - 133
242VALVALVALVALUU16 - 13910 - 133
143ILEILELEULEUBB17 - 15911 - 153
243ILEILELEULEUVV17 - 15911 - 153
144GLUGLUVALVALBB15 - 1399 - 133
244GLUGLUVALVALWW15 - 1399 - 133
145VALVALGLUGLUBB16 - 16010 - 154
245VALVALGLUGLUXX16 - 16010 - 154
146GLUGLUVALVALCC15 - 1399 - 133
246GLUGLUVALVALDD15 - 1399 - 133
147VALVALVALVALCC16 - 13910 - 133
247VALVALVALVALEE16 - 13910 - 133
148ILEILEVALVALCC17 - 13911 - 133
248ILEILEVALVALFF17 - 13911 - 133
149GLUGLUGLNGLNCC15 - 1409 - 134
249GLUGLUGLNGLNGG15 - 1409 - 134
150GLUGLUVALVALCC15 - 1399 - 133
250GLUGLUVALVALHH15 - 1399 - 133
151GLUGLUCYSCYSCC15 - 1389 - 132
251GLUGLUCYSCYSII15 - 1389 - 132
152GLUGLUVALVALCC15 - 1399 - 133
252GLUGLUVALVALJJ15 - 1399 - 133
153VALVALGLNGLNCC16 - 14010 - 134
253VALVALGLNGLNKK16 - 14010 - 134
154GLUGLUVALVALCC15 - 1399 - 133
254GLUGLUVALVALLL15 - 1399 - 133
155VALVALVALVALCC16 - 13910 - 133
255VALVALVALVALMM16 - 13910 - 133
156GLUGLUVALVALCC15 - 1399 - 133
256GLUGLUVALVALNN15 - 1399 - 133
157VALVALVALVALCC16 - 13910 - 133
257VALVALVALVALOO16 - 13910 - 133
158GLUGLUVALVALCC15 - 1399 - 133
258GLUGLUVALVALPP15 - 1399 - 133
159VALVALVALVALCC16 - 13910 - 133
259VALVALVALVALQQ16 - 13910 - 133
160VALVALVALVALCC16 - 13910 - 133
260VALVALVALVALRR16 - 13910 - 133
161VALVALCYSCYSCC16 - 13810 - 132
261VALVALCYSCYSSS16 - 13810 - 132
162VALVALVALVALCC16 - 13910 - 133
262VALVALVALVALTT16 - 13910 - 133
163VALVALGLNGLNCC16 - 14010 - 134
263VALVALGLNGLNUU16 - 14010 - 134
164ILEILEVALVALCC17 - 13911 - 133
264ILEILEVALVALVV17 - 13911 - 133
165GLUGLUGLNGLNCC15 - 1409 - 134
265GLUGLUGLNGLNWW15 - 1409 - 134
166VALVALVALVALCC16 - 13910 - 133
266VALVALVALVALXX16 - 13910 - 133
167VALVALVALVALDD16 - 13910 - 133
267VALVALVALVALEE16 - 13910 - 133
168ILEILEGLUGLUDD17 - 16011 - 154
268ILEILEGLUGLUFF17 - 16011 - 154
169GLUGLUVALVALDD15 - 1399 - 133
269GLUGLUVALVALGG15 - 1399 - 133
170GLUGLUGLUGLUDD15 - 1609 - 154
270GLUGLUGLUGLUHH15 - 1609 - 154
171GLUGLUCYSCYSDD15 - 1389 - 132
271GLUGLUCYSCYSII15 - 1389 - 132
172GLUGLUGLUGLUDD14 - 1608 - 154
272GLUGLUGLUGLUJJ14 - 1608 - 154
173VALVALVALVALDD16 - 13910 - 133
273VALVALVALVALKK16 - 13910 - 133
174GLUGLUGLUGLUDD15 - 1609 - 154
274GLUGLUGLUGLULL15 - 1609 - 154
175VALVALVALVALDD16 - 13910 - 133
275VALVALVALVALMM16 - 13910 - 133
176GLUGLULEULEUDD14 - 1598 - 153
276GLUGLULEULEUNN14 - 1598 - 153
177VALVALCYSCYSDD16 - 13810 - 132
277VALVALCYSCYSOO16 - 13810 - 132
178GLUGLULEULEUDD15 - 1599 - 153
278GLUGLULEULEUPP15 - 1599 - 153
179VALVALCYSCYSDD16 - 13810 - 132
279VALVALCYSCYSQQ16 - 13810 - 132
180VALVALLEULEUDD16 - 15910 - 153
280VALVALLEULEURR16 - 15910 - 153
181VALVALCYSCYSDD16 - 13810 - 132
281VALVALCYSCYSSS16 - 13810 - 132
182VALVALGLUGLUDD16 - 16010 - 154
282VALVALGLUGLUTT16 - 16010 - 154
183VALVALVALVALDD16 - 13910 - 133
283VALVALVALVALUU16 - 13910 - 133
184ILEILELEULEUDD17 - 15911 - 153
284ILEILELEULEUVV17 - 15911 - 153
185GLUGLUVALVALDD15 - 1399 - 133
285GLUGLUVALVALWW15 - 1399 - 133
186VALVALGLUGLUDD16 - 16010 - 154
286VALVALGLUGLUXX16 - 16010 - 154
187ILEILEVALVALEE17 - 13911 - 133
287ILEILEVALVALFF17 - 13911 - 133
188VALVALVALVALEE16 - 13910 - 133
288VALVALVALVALGG16 - 13910 - 133
189VALVALVALVALEE16 - 13910 - 133
289VALVALVALVALHH16 - 13910 - 133
190VALVALCYSCYSEE16 - 13810 - 132
290VALVALCYSCYSII16 - 13810 - 132
191VALVALVALVALEE16 - 13910 - 133
291VALVALVALVALJJ16 - 13910 - 133
192VALVALGLNGLNEE16 - 14010 - 134
292VALVALGLNGLNKK16 - 14010 - 134
193VALVALVALVALEE16 - 13910 - 133
293VALVALVALVALLL16 - 13910 - 133
194VALVALGLNGLNEE16 - 14010 - 134
294VALVALGLNGLNMM16 - 14010 - 134
195VALVALVALVALEE16 - 13910 - 133
295VALVALVALVALNN16 - 13910 - 133
196VALVALVALVALEE16 - 13910 - 133
296VALVALVALVALOO16 - 13910 - 133
197VALVALVALVALEE16 - 13910 - 133
297VALVALVALVALPP16 - 13910 - 133
198VALVALVALVALEE16 - 13910 - 133
298VALVALVALVALQQ16 - 13910 - 133
199VALVALVALVALEE16 - 13910 - 133
299VALVALVALVALRR16 - 13910 - 133
1100VALVALCYSCYSEE16 - 13810 - 132
2100VALVALCYSCYSSS16 - 13810 - 132
1101VALVALVALVALEE16 - 13910 - 133
2101VALVALVALVALTT16 - 13910 - 133
1102VALVALGLNGLNEE16 - 14010 - 134
2102VALVALGLNGLNUU16 - 14010 - 134
1103ILEILEVALVALEE17 - 13911 - 133
2103ILEILEVALVALVV17 - 13911 - 133
1104VALVALGLNGLNEE16 - 14010 - 134
2104VALVALGLNGLNWW16 - 14010 - 134
1105VALVALVALVALEE16 - 13910 - 133
2105VALVALVALVALXX16 - 13910 - 133
1106ILEILEVALVALFF17 - 13911 - 133
2106ILEILEVALVALGG17 - 13911 - 133
1107ILEILEGLUGLUFF17 - 16011 - 154
2107ILEILEGLUGLUHH17 - 16011 - 154
1108ILEILECYSCYSFF17 - 13811 - 132
2108ILEILECYSCYSII17 - 13811 - 132
1109ILEILELEULEUFF17 - 15911 - 153
2109ILEILELEULEUJJ17 - 15911 - 153
1110ILEILEVALVALFF17 - 13911 - 133
2110ILEILEVALVALKK17 - 13911 - 133
1111ILEILEGLUGLUFF17 - 16011 - 154
2111ILEILEGLUGLULL17 - 16011 - 154
1112ILEILEVALVALFF17 - 13911 - 133
2112ILEILEVALVALMM17 - 13911 - 133
1113ILEILEASNASNFF17 - 15811 - 152
2113ILEILEASNASNNN17 - 15811 - 152
1114ILEILECYSCYSFF17 - 13811 - 132
2114ILEILECYSCYSOO17 - 13811 - 132
1115ILEILEASNASNFF17 - 15811 - 152
2115ILEILEASNASNPP17 - 15811 - 152
1116ILEILECYSCYSFF17 - 13811 - 132
2116ILEILECYSCYSQQ17 - 13811 - 132
1117ILEILEASNASNFF17 - 15811 - 152
2117ILEILEASNASNRR17 - 15811 - 152
1118ILEILECYSCYSFF17 - 13811 - 132
2118ILEILECYSCYSSS17 - 13811 - 132
1119ILEILEGLUGLUFF17 - 16011 - 154
2119ILEILEGLUGLUTT17 - 16011 - 154
1120ILEILEVALVALFF17 - 13911 - 133
2120ILEILEVALVALUU17 - 13911 - 133
1121ILEILELEULEUFF17 - 15911 - 153
2121ILEILELEULEUVV17 - 15911 - 153
1122ILEILEVALVALFF17 - 13911 - 133
2122ILEILEVALVALWW17 - 13911 - 133
1123ILEILEGLUGLUFF17 - 16011 - 154
2123ILEILEGLUGLUXX17 - 16011 - 154
1124GLUGLUVALVALGG15 - 1399 - 133
2124GLUGLUVALVALHH15 - 1399 - 133
1125GLUGLUCYSCYSGG15 - 1389 - 132
2125GLUGLUCYSCYSII15 - 1389 - 132
1126GLUGLUVALVALGG15 - 1399 - 133
2126GLUGLUVALVALJJ15 - 1399 - 133
1127VALVALGLNGLNGG16 - 14010 - 134
2127VALVALGLNGLNKK16 - 14010 - 134
1128GLUGLUVALVALGG15 - 1399 - 133
2128GLUGLUVALVALLL15 - 1399 - 133
1129VALVALVALVALGG16 - 13910 - 133
2129VALVALVALVALMM16 - 13910 - 133
1130GLUGLUVALVALGG15 - 1399 - 133
2130GLUGLUVALVALNN15 - 1399 - 133
1131VALVALVALVALGG16 - 13910 - 133
2131VALVALVALVALOO16 - 13910 - 133
1132GLUGLUVALVALGG15 - 1399 - 133
2132GLUGLUVALVALPP15 - 1399 - 133
1133VALVALVALVALGG16 - 13910 - 133
2133VALVALVALVALQQ16 - 13910 - 133
1134VALVALVALVALGG16 - 13910 - 133
2134VALVALVALVALRR16 - 13910 - 133
1135VALVALCYSCYSGG16 - 13810 - 132
2135VALVALCYSCYSSS16 - 13810 - 132
1136VALVALVALVALGG16 - 13910 - 133
2136VALVALVALVALTT16 - 13910 - 133
1137VALVALGLNGLNGG16 - 14010 - 134
2137VALVALGLNGLNUU16 - 14010 - 134
1138ILEILEVALVALGG17 - 13911 - 133
2138ILEILEVALVALVV17 - 13911 - 133
1139GLUGLUGLNGLNGG15 - 1409 - 134
2139GLUGLUGLNGLNWW15 - 1409 - 134
1140VALVALVALVALGG16 - 13910 - 133
2140VALVALVALVALXX16 - 13910 - 133
1141GLUGLUCYSCYSHH15 - 1389 - 132
2141GLUGLUCYSCYSII15 - 1389 - 132
1142GLUGLUGLUGLUHH15 - 1609 - 154
2142GLUGLUGLUGLUJJ15 - 1609 - 154
1143VALVALVALVALHH16 - 13910 - 133
2143VALVALVALVALKK16 - 13910 - 133
1144GLUGLUGLUGLUHH15 - 1609 - 154
2144GLUGLUGLUGLULL15 - 1609 - 154
1145VALVALVALVALHH16 - 13910 - 133
2145VALVALVALVALMM16 - 13910 - 133
1146GLUGLULEULEUHH15 - 1599 - 153
2146GLUGLULEULEUNN15 - 1599 - 153
1147VALVALCYSCYSHH16 - 13810 - 132
2147VALVALCYSCYSOO16 - 13810 - 132
1148GLUGLULEULEUHH15 - 1599 - 153
2148GLUGLULEULEUPP15 - 1599 - 153
1149VALVALCYSCYSHH16 - 13810 - 132
2149VALVALCYSCYSQQ16 - 13810 - 132
1150VALVALLEULEUHH16 - 15910 - 153
2150VALVALLEULEURR16 - 15910 - 153
1151VALVALCYSCYSHH16 - 13810 - 132
2151VALVALCYSCYSSS16 - 13810 - 132
1152VALVALLEULEUHH16 - 15910 - 153
2152VALVALLEULEUTT16 - 15910 - 153
1153VALVALVALVALHH16 - 13910 - 133
2153VALVALVALVALUU16 - 13910 - 133
1154ILEILELEULEUHH17 - 15911 - 153
2154ILEILELEULEUVV17 - 15911 - 153
1155GLUGLUVALVALHH15 - 1399 - 133
2155GLUGLUVALVALWW15 - 1399 - 133
1156VALVALGLUGLUHH16 - 16010 - 154
2156VALVALGLUGLUXX16 - 16010 - 154
1157GLUGLUCYSCYSII15 - 1389 - 132
2157GLUGLUCYSCYSJJ15 - 1389 - 132
1158VALVALVALVALII16 - 13910 - 133
2158VALVALVALVALKK16 - 13910 - 133
1159GLUGLUCYSCYSII15 - 1389 - 132
2159GLUGLUCYSCYSLL15 - 1389 - 132
1160VALVALCYSCYSII16 - 13810 - 132
2160VALVALCYSCYSMM16 - 13810 - 132
1161GLUGLUCYSCYSII15 - 1389 - 132
2161GLUGLUCYSCYSNN15 - 1389 - 132
1162VALVALVALVALII16 - 13910 - 133
2162VALVALVALVALOO16 - 13910 - 133
1163GLUGLUCYSCYSII15 - 1389 - 132
2163GLUGLUCYSCYSPP15 - 1389 - 132
1164VALVALVALVALII16 - 13910 - 133
2164VALVALVALVALQQ16 - 13910 - 133
1165VALVALCYSCYSII16 - 13810 - 132
2165VALVALCYSCYSRR16 - 13810 - 132
1166VALVALCYSCYSII16 - 13810 - 132
2166VALVALCYSCYSSS16 - 13810 - 132
1167VALVALCYSCYSII16 - 13810 - 132
2167VALVALCYSCYSTT16 - 13810 - 132
1168VALVALVALVALII16 - 13910 - 133
2168VALVALVALVALUU16 - 13910 - 133
1169ILEILECYSCYSII17 - 13811 - 132
2169ILEILECYSCYSVV17 - 13811 - 132
1170GLUGLUVALVALII15 - 1399 - 133
2170GLUGLUVALVALWW15 - 1399 - 133
1171VALVALCYSCYSII16 - 13810 - 132
2171VALVALCYSCYSXX16 - 13810 - 132
1172VALVALVALVALJJ16 - 13910 - 133
2172VALVALVALVALKK16 - 13910 - 133
1173GLUGLUGLUGLUJJ15 - 1609 - 154
2173GLUGLUGLUGLULL15 - 1609 - 154
1174VALVALVALVALJJ16 - 13910 - 133
2174VALVALVALVALMM16 - 13910 - 133
1175GLUGLULEULEUJJ14 - 1598 - 153
2175GLUGLULEULEUNN14 - 1598 - 153
1176VALVALCYSCYSJJ16 - 13810 - 132
2176VALVALCYSCYSOO16 - 13810 - 132
1177GLUGLULEULEUJJ15 - 1599 - 153
2177GLUGLULEULEUPP15 - 1599 - 153
1178VALVALCYSCYSJJ16 - 13810 - 132
2178VALVALCYSCYSQQ16 - 13810 - 132
1179VALVALASNASNJJ16 - 15810 - 152
2179VALVALASNASNRR16 - 15810 - 152
1180VALVALCYSCYSJJ16 - 13810 - 132
2180VALVALCYSCYSSS16 - 13810 - 132
1181VALVALGLUGLUJJ16 - 16010 - 154
2181VALVALGLUGLUTT16 - 16010 - 154
1182VALVALVALVALJJ16 - 13910 - 133
2182VALVALVALVALUU16 - 13910 - 133
1183ILEILELEULEUJJ17 - 15911 - 153
2183ILEILELEULEUVV17 - 15911 - 153
1184GLUGLUVALVALJJ15 - 1399 - 133
2184GLUGLUVALVALWW15 - 1399 - 133
1185VALVALGLUGLUJJ16 - 16010 - 154
2185VALVALGLUGLUXX16 - 16010 - 154
1186VALVALVALVALKK16 - 13910 - 133
2186VALVALVALVALLL16 - 13910 - 133
1187VALVALGLNGLNKK16 - 14010 - 134
2187VALVALGLNGLNMM16 - 14010 - 134
1188VALVALVALVALKK16 - 13910 - 133
2188VALVALVALVALNN16 - 13910 - 133
1189VALVALVALVALKK16 - 13910 - 133
2189VALVALVALVALOO16 - 13910 - 133
1190VALVALVALVALKK16 - 13910 - 133
2190VALVALVALVALPP16 - 13910 - 133
1191VALVALVALVALKK16 - 13910 - 133
2191VALVALVALVALQQ16 - 13910 - 133
1192VALVALVALVALKK16 - 13910 - 133
2192VALVALVALVALRR16 - 13910 - 133
1193VALVALVALVALKK16 - 13910 - 133
2193VALVALVALVALSS16 - 13910 - 133
1194VALVALVALVALKK16 - 13910 - 133
2194VALVALVALVALTT16 - 13910 - 133
1195VALVALGLNGLNKK16 - 14010 - 134
2195VALVALGLNGLNUU16 - 14010 - 134
1196ILEILEVALVALKK17 - 13911 - 133
2196ILEILEVALVALVV17 - 13911 - 133
1197VALVALGLNGLNKK16 - 14010 - 134
2197VALVALGLNGLNWW16 - 14010 - 134
1198VALVALVALVALKK16 - 13910 - 133
2198VALVALVALVALXX16 - 13910 - 133
1199VALVALVALVALLL16 - 13910 - 133
2199VALVALVALVALMM16 - 13910 - 133
1200GLUGLULEULEULL15 - 1599 - 153
2200GLUGLULEULEUNN15 - 1599 - 153
1201VALVALCYSCYSLL16 - 13810 - 132
2201VALVALCYSCYSOO16 - 13810 - 132
1202GLUGLULEULEULL15 - 1599 - 153
2202GLUGLULEULEUPP15 - 1599 - 153
1203VALVALCYSCYSLL16 - 13810 - 132
2203VALVALCYSCYSQQ16 - 13810 - 132
1204VALVALLEULEULL16 - 15910 - 153
2204VALVALLEULEURR16 - 15910 - 153
1205VALVALCYSCYSLL16 - 13810 - 132
2205VALVALCYSCYSSS16 - 13810 - 132
1206VALVALGLUGLULL16 - 16010 - 154
2206VALVALGLUGLUTT16 - 16010 - 154
1207VALVALVALVALLL16 - 13910 - 133
2207VALVALVALVALUU16 - 13910 - 133
1208ILEILELEULEULL17 - 15911 - 153
2208ILEILELEULEUVV17 - 15911 - 153
1209GLUGLUVALVALLL15 - 1399 - 133
2209GLUGLUVALVALWW15 - 1399 - 133
1210VALVALGLUGLULL16 - 16010 - 154
2210VALVALGLUGLUXX16 - 16010 - 154
1211VALVALVALVALMM16 - 13910 - 133
2211VALVALVALVALNN16 - 13910 - 133
1212VALVALVALVALMM16 - 13910 - 133
2212VALVALVALVALOO16 - 13910 - 133
1213VALVALVALVALMM16 - 13910 - 133
2213VALVALVALVALPP16 - 13910 - 133
1214VALVALVALVALMM16 - 13910 - 133
2214VALVALVALVALQQ16 - 13910 - 133
1215VALVALVALVALMM16 - 13910 - 133
2215VALVALVALVALRR16 - 13910 - 133
1216VALVALCYSCYSMM16 - 13810 - 132
2216VALVALCYSCYSSS16 - 13810 - 132
1217VALVALVALVALMM16 - 13910 - 133
2217VALVALVALVALTT16 - 13910 - 133
1218VALVALGLNGLNMM16 - 14010 - 134
2218VALVALGLNGLNUU16 - 14010 - 134
1219ILEILEVALVALMM17 - 13911 - 133
2219ILEILEVALVALVV17 - 13911 - 133
1220VALVALGLNGLNMM16 - 14010 - 134
2220VALVALGLNGLNWW16 - 14010 - 134
1221VALVALVALVALMM16 - 13910 - 133
2221VALVALVALVALXX16 - 13910 - 133
1222VALVALCYSCYSNN16 - 13810 - 132
2222VALVALCYSCYSOO16 - 13810 - 132
1223GLUGLULEULEUNN15 - 1599 - 153
2223GLUGLULEULEUPP15 - 1599 - 153
1224VALVALCYSCYSNN16 - 13810 - 132
2224VALVALCYSCYSQQ16 - 13810 - 132
1225VALVALASNASNNN16 - 15810 - 152
2225VALVALASNASNRR16 - 15810 - 152
1226VALVALCYSCYSNN16 - 13810 - 132
2226VALVALCYSCYSSS16 - 13810 - 132
1227VALVALLEULEUNN16 - 15910 - 153
2227VALVALLEULEUTT16 - 15910 - 153
1228VALVALVALVALNN16 - 13910 - 133
2228VALVALVALVALUU16 - 13910 - 133
1229ILEILELEULEUNN17 - 15911 - 153
2229ILEILELEULEUVV17 - 15911 - 153
1230GLUGLUVALVALNN15 - 1399 - 133
2230GLUGLUVALVALWW15 - 1399 - 133
1231VALVALASNASNNN16 - 15810 - 152
2231VALVALASNASNXX16 - 15810 - 152
1232VALVALCYSCYSOO16 - 13810 - 132
2232VALVALCYSCYSPP16 - 13810 - 132
1233VALVALVALVALOO16 - 13910 - 133
2233VALVALVALVALQQ16 - 13910 - 133
1234VALVALCYSCYSOO16 - 13810 - 132
2234VALVALCYSCYSRR16 - 13810 - 132
1235VALVALVALVALOO16 - 13910 - 133
2235VALVALVALVALSS16 - 13910 - 133
1236VALVALCYSCYSOO16 - 13810 - 132
2236VALVALCYSCYSTT16 - 13810 - 132
1237VALVALVALVALOO16 - 13910 - 133
2237VALVALVALVALUU16 - 13910 - 133
1238ILEILECYSCYSOO17 - 13811 - 132
2238ILEILECYSCYSVV17 - 13811 - 132
1239VALVALVALVALOO16 - 13910 - 133
2239VALVALVALVALWW16 - 13910 - 133
1240VALVALCYSCYSOO16 - 13810 - 132
2240VALVALCYSCYSXX16 - 13810 - 132
1241VALVALCYSCYSPP16 - 13810 - 132
2241VALVALCYSCYSQQ16 - 13810 - 132
1242VALVALLEULEUPP16 - 15910 - 153
2242VALVALLEULEURR16 - 15910 - 153
1243VALVALCYSCYSPP16 - 13810 - 132
2243VALVALCYSCYSSS16 - 13810 - 132
1244VALVALLEULEUPP16 - 15910 - 153
2244VALVALLEULEUTT16 - 15910 - 153
1245VALVALVALVALPP16 - 13910 - 133
2245VALVALVALVALUU16 - 13910 - 133
1246ILEILELEULEUPP17 - 15911 - 153
2246ILEILELEULEUVV17 - 15911 - 153
1247GLUGLUVALVALPP15 - 1399 - 133
2247GLUGLUVALVALWW15 - 1399 - 133
1248VALVALASNASNPP16 - 15810 - 152
2248VALVALASNASNXX16 - 15810 - 152
1249VALVALCYSCYSQQ16 - 13810 - 132
2249VALVALCYSCYSRR16 - 13810 - 132
1250VALVALVALVALQQ16 - 13910 - 133
2250VALVALVALVALSS16 - 13910 - 133
1251VALVALCYSCYSQQ16 - 13810 - 132
2251VALVALCYSCYSTT16 - 13810 - 132
1252VALVALVALVALQQ16 - 13910 - 133
2252VALVALVALVALUU16 - 13910 - 133
1253ILEILECYSCYSQQ17 - 13811 - 132
2253ILEILECYSCYSVV17 - 13811 - 132
1254VALVALVALVALQQ16 - 13910 - 133
2254VALVALVALVALWW16 - 13910 - 133
1255VALVALCYSCYSQQ16 - 13810 - 132
2255VALVALCYSCYSXX16 - 13810 - 132
1256VALVALCYSCYSRR16 - 13810 - 132
2256VALVALCYSCYSSS16 - 13810 - 132
1257VALVALLEULEURR16 - 15910 - 153
2257VALVALLEULEUTT16 - 15910 - 153
1258VALVALVALVALRR16 - 13910 - 133
2258VALVALVALVALUU16 - 13910 - 133
1259ILEILELEULEURR17 - 15911 - 153
2259ILEILELEULEUVV17 - 15911 - 153
1260VALVALVALVALRR16 - 13910 - 133
2260VALVALVALVALWW16 - 13910 - 133
1261VALVALLEULEURR16 - 15910 - 153
2261VALVALLEULEUXX16 - 15910 - 153
1262VALVALCYSCYSSS16 - 13810 - 132
2262VALVALCYSCYSTT16 - 13810 - 132
1263VALVALVALVALSS16 - 13910 - 133
2263VALVALVALVALUU16 - 13910 - 133
1264ILEILECYSCYSSS17 - 13811 - 132
2264ILEILECYSCYSVV17 - 13811 - 132
1265VALVALVALVALSS16 - 13910 - 133
2265VALVALVALVALWW16 - 13910 - 133
1266VALVALCYSCYSSS16 - 13810 - 132
2266VALVALCYSCYSXX16 - 13810 - 132
1267VALVALVALVALTT16 - 13910 - 133
2267VALVALVALVALUU16 - 13910 - 133
1268ILEILELEULEUTT17 - 15911 - 153
2268ILEILELEULEUVV17 - 15911 - 153
1269VALVALVALVALTT16 - 13910 - 133
2269VALVALVALVALWW16 - 13910 - 133
1270VALVALGLUGLUTT16 - 16010 - 154
2270VALVALGLUGLUXX16 - 16010 - 154
1271ILEILEVALVALUU17 - 13911 - 133
2271ILEILEVALVALVV17 - 13911 - 133
1272VALVALGLNGLNUU16 - 14010 - 134
2272VALVALGLNGLNWW16 - 14010 - 134
1273VALVALVALVALUU16 - 13910 - 133
2273VALVALVALVALXX16 - 13910 - 133
1274ILEILEVALVALVV17 - 13911 - 133
2274ILEILEVALVALWW17 - 13911 - 133
1275ILEILELEULEUVV17 - 15911 - 153
2275ILEILELEULEUXX17 - 15911 - 153
1276VALVALVALVALWW16 - 13910 - 133
2276VALVALVALVALXX16 - 13910 - 133

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
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276

-
Components

#1: Protein ...
Sorting nexin-11


Mass: 18831.830 Da / Num. of mol.: 24 / Fragment: PX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX11 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9Y5W9
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.57 % / Mosaicity: 0.28 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.3
Details: 0.1 M sodium acetate trihydrate pH 4.3, 1.8 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→66.54 Å / Num. obs: 80923 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Rrim(I) all: 0.143 / Net I/σ(I): 11.3 / Num. measured all: 507560 / Scaling rejects: 517
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.576.40.8192770843500.6990.3470.8922.698.6
18.19-66.545.20.07333396460.9890.0330.0822.296.7

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKB
Resolution: 3.5→65.87 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.887 / SU B: 28.827 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.549
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 3921 4.8 %RANDOM
Rwork0.2344 ---
obs0.2359 76927 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 254.7 Å2 / Biso mean: 110.066 Å2 / Biso min: 53.42 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-0 Å2-0 Å2
2---1.61 Å20 Å2
3---3.61 Å2
Refinement stepCycle: final / Resolution: 3.5→65.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25878 0 0 0 25878
Num. residues----3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01326386
X-RAY DIFFRACTIONr_bond_other_d0.0040.01724890
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.64435634
X-RAY DIFFRACTIONr_angle_other_deg1.1441.57457562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72253119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.5921.0141588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.702154740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.57215264
X-RAY DIFFRACTIONr_chiral_restr0.0770.23291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0229046
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025922
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36970.09
12B36970.09
21A38660.1
22C38660.1
31A38770.08
32D38770.08
41A38880.09
42E38880.09
51A36440.08
52F36440.08
61A38450.09
62G38450.09
71A37940.09
72H37940.09
81A38640.09
82I38640.09
91A36790.09
92J36790.09
101A37570.06
102K37570.06
111A37470.09
112L37470.09
121A39090.09
122M39090.09
131A37110.08
132N37110.08
141A37730.08
142O37730.08
151A37040.09
152P37040.09
161A38470.08
162Q38470.08
171A36950.08
172R36950.08
181A39340.07
182S39340.07
191A37500.08
192T37500.08
201A38110.09
202U38110.09
211A35020.06
212V35020.06
221A37970.07
222W37970.07
231A37160.09
232X37160.09
241B37220.1
242C37220.1
251B43170.09
252D43170.09
261B37220.08
262E37220.08
271B42330.09
272F42330.09
281B37420.08
282G37420.08
291B43140.1
292H43140.1
301B36880.08
302I36880.08
311B43410.08
312J43410.08
321B36310.06
322K36310.06
331B43250.09
332L43250.09
341B37370.09
342M37370.09
351B43200.07
352N43200.07
361B36060.07
362O36060.07
371B42960.1
372P42960.1
381B36690.08
382Q36690.08
391B42190.1
392R42190.1
401B36960.08
402S36960.08
411B43010.09
412T43010.09
421B36150.09
422U36150.09
431B40300.08
432V40300.08
441B37160.08
442W37160.08
451B42860.09
452X42860.09
461C39030.11
462D39030.11
471C39680.08
472E39680.08
481C36590.09
482F36590.09
491C39790.09
492G39790.09
501C38370.1
502H38370.1
511C38700.1
512I38700.1
521C37130.1
522J37130.1
531C37860.07
532K37860.07
541C38090.1
542L38090.1
551C39430.09
552M39430.09
561C37710.09
562N37710.09
571C37630.07
572O37630.07
581C37630.1
582P37630.1
591C38670.08
592Q38670.08
601C37090.09
602R37090.09
611C38930.09
612S38930.09
621C37580.1
622T37580.1
631C38870.09
632U38870.09
641C35270.08
642V35270.08
651C38890.07
652W38890.07
661C37280.1
662X37280.1
671D39060.09
672E39060.09
681D42840.07
682F42840.07
691D38930.09
692G38930.09
701D44230.09
702H44230.09
711D38200.09
712I38200.09
721D43550.09
722J43550.09
731D37420.07
732K37420.07
741D43820.09
742L43820.09
751D39060.09
752M39060.09
761D43530.08
762N43530.08
771D37230.08
772O37230.08
781D43380.09
782P43380.09
791D37830.08
792Q37830.08
801D42610.1
802R42610.1
811D38770.08
812S38770.08
821D43590.07
822T43590.07
831D37700.1
832U37700.1
841D40250.08
842V40250.08
851D37930.08
852W37930.08
861D43660.08
862X43660.08
871E36920.08
872F36920.08
881E39430.07
882G39430.07
891E38450.08
892H38450.08
901E38800.06
902I38800.06
911E37250.09
912J37250.09
921E37870.07
922K37870.07
931E37990.09
932L37990.09
941E39490.09
942M39490.09
951E37570.07
952N37570.07
961E37920.06
962O37920.06
971E37460.09
972P37460.09
981E38640.08
982Q38640.08
991E37290.08
992R37290.08
1001E39040.07
1002S39040.07
1011E37920.09
1012T37920.09
1021E38550.08
1022U38550.08
1031E35420.07
1032V35420.07
1041E38630.06
1042W38630.06
1051E37580.09
1052X37580.09
1061F36920.08
1062G36920.08
1071F42470.08
1072H42470.08
1081F36200.08
1082I36200.08
1091F42670.07
1092J42670.07
1101F35850.07
1102K35850.07
1111F42300.1
1112L42300.1
1121F36980.09
1122M36980.09
1131F42290.08
1132N42290.08
1141F35650.07
1142O35650.07
1151F42080.09
1152P42080.09
1161F36300.08
1162Q36300.08
1171F41890.1
1172R41890.1
1181F36550.08
1182S36550.08
1191F42370.08
1192T42370.08
1201F35770.09
1202U35770.09
1211F39900.08
1212V39900.08
1221F36690.08
1222W36690.08
1231F42110.1
1232X42110.1
1241G38580.08
1242H38580.08
1251G38770.07
1252I38770.07
1261G37430.09
1262J37430.09
1271G37770.06
1272K37770.06
1281G38380.08
1282L38380.08
1291G38940.09
1292M38940.09
1301G37980.07
1302N37980.07
1311G37890.06
1312O37890.06
1321G37860.09
1322P37860.09
1331G38710.08
1332Q38710.08
1341G37220.08
1342R37220.08
1351G38780.08
1352S38780.08
1361G37840.09
1362T37840.09
1371G38490.08
1372U38490.08
1381G35300.07
1382V35300.07
1391G38930.06
1392W38930.06
1401G37390.09
1402X37390.09
1411H37860.08
1412I37860.08
1421H43180.09
1422J43180.09
1431H37280.07
1432K37280.07
1441H44040.09
1442L44040.09
1451H38380.09
1452M38380.09
1461H43330.08
1462N43330.08
1471H37180.07
1472O37180.07
1481H43170.1
1482P43170.1
1491H37620.09
1492Q37620.09
1501H42670.1
1502R42670.1
1511H38100.08
1512S38100.08
1521H43210.09
1522T43210.09
1531H37160.1
1532U37160.1
1541H39980.09
1542V39980.09
1551H37990.08
1552W37990.08
1561H43200.1
1562X43200.1
1571I36700.09
1572J36700.09
1581I37220.06
1582K37220.06
1591I37390.09
1592L37390.09
1601I38410.09
1602M38410.09
1611I37090.07
1612N37090.07
1621I37540.06
1622O37540.06
1631I37170.09
1632P37170.09
1641I38420.08
1642Q38420.08
1651I37020.08
1652R37020.08
1661I38690.09
1662S38690.09
1671I37460.08
1672T37460.08
1681I37980.09
1682U37980.09
1691I34750.06
1692V34750.06
1701I37840.08
1702W37840.08
1711I37110.08
1712X37110.08
1721J36250.07
1722K36250.07
1731J43200.09
1732L43200.09
1741J37210.09
1742M37210.09
1751J43640.08
1752N43640.08
1761J36180.07
1762O36180.07
1771J42810.09
1772P42810.09
1781J36620.09
1782Q36620.09
1791J42400.09
1792R42400.09
1801J36910.08
1802S36910.08
1811J43080.09
1812T43080.09
1821J36110.09
1822U36110.09
1831J40420.07
1832V40420.07
1841J37180.09
1842W37180.09
1851J42990.09
1852X42990.09
1861K36920.08
1862L36920.08
1871K37960.06
1872M37960.06
1881K36380.06
1882N36380.06
1891K37840.05
1892O37840.05
1901K36370.07
1902P36370.07
1911K37430.05
1912Q37430.05
1921K36150.06
1922R36150.06
1931K37670.06
1932S37670.06
1941K36690.07
1942T36690.07
1951K37730.07
1952U37730.07
1961K35450.06
1962V35450.06
1971K37470.05
1972W37470.05
1981K36380.08
1982X36380.08
1991L37900.1
1992M37900.1
2001L43640.07
2002N43640.07
2011L36700.08
2012O36700.08
2021L43510.09
2022P43510.09
2031L37540.09
2032Q37540.09
2041L42320.1
2042R42320.1
2051L37610.09
2052S37610.09
2061L43080.1
2062T43080.1
2071L37010.09
2072U37010.09
2081L40120.08
2082V40120.08
2091L37980.09
2092W37980.09
2101L43060.1
2102X43060.1
2111M37620.08
2112N37620.08
2121M37960.07
2122O37960.07
2131M37460.1
2132P37460.1
2141M38580.08
2142Q38580.08
2151M37320.09
2152R37320.09
2161M39160.08
2162S39160.08
2171M37940.09
2172T37940.09
2181M38460.09
2182U38460.09
2191M35460.07
2192V35460.07
2201M38290.08
2202W38290.08
2211M37600.09
2212X37600.09
2221N36280.07
2222O36280.07
2231N43540.08
2232P43540.08
2241N37110.07
2242Q37110.07
2251N42610.09
2252R42610.09
2261N37240.07
2262S37240.07
2271N43000.08
2272T43000.08
2281N36590.08
2282U36590.08
2291N40250.07
2292V40250.07
2301N37700.07
2302W37700.07
2311N42780.08
2312X42780.08
2321O36240.09
2322P36240.09
2331O37380.07
2332Q37380.07
2341O36040.07
2342R36040.07
2351O37920.07
2352S37920.07
2361O36590.08
2362T36590.08
2371O37480.07
2372U37480.07
2381O35320.06
2382V35320.06
2391O37170.05
2392W37170.05
2401O36280.08
2402X36280.08
2411P37240.08
2412Q37240.08
2421P42650.11
2422R42650.11
2431P37430.09
2432S37430.09
2441P43240.09
2442T43240.09
2451P36840.09
2452U36840.09
2461P40020.08
2462V40020.08
2471P37570.08
2472W37570.08
2481P43000.09
2482X43000.09
2491Q36920.07
2492R36920.07
2501Q38840.08
2502S38840.08
2511Q37350.08
2512T37350.08
2521Q38100.06
2522U38100.06
2531Q34900.06
2532V34900.06
2541Q38190.07
2542W38190.07
2551Q37070.08
2552X37070.08
2561R37350.08
2562S37350.08
2571R42600.1
2572T42600.1
2581R36490.08
2582U36490.08
2591R39740.1
2592V39740.1
2601R37020.08
2602W37020.08
2611R42500.11
2612X42500.11
2621S37900.08
2622T37900.08
2631S38810.07
2632U38810.07
2641S35160.06
2642V35160.06
2651S38320.05
2652W38320.05
2661S37590.08
2662X37590.08
2671T37070.1
2672U37070.1
2681T40360.07
2682V40360.07
2691T37290.08
2692W37290.08
2701T43500.08
2702X43500.08
2711U35190.08
2712V35190.08
2721U37780.06
2722W37780.06
2731U36630.1
2732X36630.1
2741V35420.07
2742W35420.07
2751V40400.07
2752X40400.07
2761W37150.09
2762X37150.09
LS refinement shellResolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 309 -
Rwork0.339 5576 -
all-5885 -
obs--98.77 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more