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- PDB-5dtl: Crystal structure of mEos2-A69T fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 5dtl
TitleCrystal structure of mEos2-A69T fluorescent protein
ComponentsGreen to red photoconvertible GFP-like protein EosFP
KeywordsFLUORESCENT PROTEIN / mEos2 / blinking
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBerardozzi, R. / Adam, V. / Martins, A. / Bourgeois, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins.
Authors: Berardozzi, R. / Adam, V. / Martins, A. / Bourgeois, D.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 2.0Sep 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.mon_id
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Green to red photoconvertible GFP-like protein EosFP
B: Green to red photoconvertible GFP-like protein EosFP
C: Green to red photoconvertible GFP-like protein EosFP
D: Green to red photoconvertible GFP-like protein EosFP
E: Green to red photoconvertible GFP-like protein EosFP
F: Green to red photoconvertible GFP-like protein EosFP
G: Green to red photoconvertible GFP-like protein EosFP
H: Green to red photoconvertible GFP-like protein EosFP
I: Green to red photoconvertible GFP-like protein EosFP
J: Green to red photoconvertible GFP-like protein EosFP
K: Green to red photoconvertible GFP-like protein EosFP
L: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)310,72112
Polymers310,72112
Non-polymers00
Water8,485471
1
A: Green to red photoconvertible GFP-like protein EosFP
D: Green to red photoconvertible GFP-like protein EosFP
E: Green to red photoconvertible GFP-like protein EosFP
J: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)103,5744
Polymers103,5744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-27 kcal/mol
Surface area33980 Å2
MethodPISA
2
B: Green to red photoconvertible GFP-like protein EosFP
F: Green to red photoconvertible GFP-like protein EosFP
G: Green to red photoconvertible GFP-like protein EosFP
K: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)103,5744
Polymers103,5744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-26 kcal/mol
Surface area34230 Å2
MethodPISA
3
C: Green to red photoconvertible GFP-like protein EosFP
H: Green to red photoconvertible GFP-like protein EosFP
I: Green to red photoconvertible GFP-like protein EosFP
L: Green to red photoconvertible GFP-like protein EosFP


Theoretical massNumber of molelcules
Total (without water)103,5744
Polymers103,5744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-32 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.370, 96.500, 100.060
Angle α, β, γ (deg.)91.68, 107.83, 97.38
Int Tables number1
Space group name H-MP1
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
212B
113A
213C
114A
214D
115A
215E
116A
216F
117A
217G
118A
218H
119A
219I
120A
220J
121A
221K
122A
222L
123B
223C
124B
224D
125B
225E
126B
226F
127B
227G
128B
228H
129B
229I
130B
230J
131B
231K
132B
232L
133B
233C
134B
234D
135B
235E
136B
236F
137B
237G
138B
238H
139B
239I
140B
240J
141B
241K
142B
242L
143C
243D
144C
244E
145C
245F
146C
246G
147C
247H
148C
248I
149C
249J
150C
250K
151C
251L
152C
252D
153C
253E
154C
254F
155C
255G
156C
256H
157C
257I
158C
258J
159C
259K
160C
260L
161D
261E
162D
262F
163D
263G
164D
264H
165D
265I
166D
266J
167D
267K
168D
268L
169D
269E
170D
270F
171D
271G
172D
272H
173D
273I
174D
274J
175D
275K
176D
276L
177E
277F
178E
278G
179E
279H
180E
280I
181E
281J
182E
282K
183E
283L
184E
284F
185E
285G
186E
286H
187E
287I
188E
288J
189E
289K
190E
290L
191F
291G
192F
292H
193F
293I
194F
294J
195F
295K
196F
296L
197F
297G
198F
298H
199F
299I
1100F
2100J
1101F
2101K
1102F
2102L
1103G
2103H
1104G
2104I
1105G
2105J
1106G
2106K
1107G
2107L
1108G
2108H
1109G
2109I
1110G
2110J
1111G
2111K
1112G
2112L
1113H
2113I
1114H
2114J
1115H
2115K
1116H
2116L
1117H
2117I
1118H
2118J
1119H
2119K
1120H
2120L
1121I
2121J
1122I
2122K
1123I
2123L
1124I
2124J
1125I
2125K
1126I
2126L
1127J
2127K
1128J
2128L
1129J
2129K
1130J
2130L
1131K
2131L
1132K
2132L

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
11SERSERPHEPHEAA2 - 612 - 61
21SERSERPHEPHEBB2 - 612 - 61
12SERSERPHEPHEAA2 - 612 - 61
22SERSERPHEPHECC2 - 612 - 61
13SERSERPHEPHEAA2 - 612 - 61
23SERSERPHEPHEDD2 - 612 - 61
14SERSERPHEPHEAA2 - 612 - 61
24SERSERPHEPHEEE2 - 612 - 61
15SERSERPHEPHEAA2 - 612 - 61
25SERSERPHEPHEFF2 - 612 - 61
16SERSERPHEPHEAA2 - 612 - 61
26SERSERPHEPHEGG2 - 612 - 61
17SERSERPHEPHEAA2 - 612 - 61
27SERSERPHEPHEHH2 - 612 - 61
18SERSERPHEPHEAA2 - 612 - 61
28SERSERPHEPHEII2 - 612 - 61
19SERSERPHEPHEAA2 - 612 - 61
29SERSERPHEPHEJJ2 - 612 - 61
110SERSERPHEPHEAA2 - 612 - 61
210SERSERPHEPHEKK2 - 612 - 61
111SERSERPHEPHEAA2 - 612 - 61
211SERSERPHEPHELL2 - 612 - 61
112ASNASNASNASNAA65 - 22363 - 221
212ASNASNASNASNBB65 - 22363 - 221
113ASNASNASNASNAA65 - 22363 - 221
213ASNASNASNASNCC65 - 22363 - 221
114ASNASNASNASNAA65 - 22363 - 221
214ASNASNASNASNDD65 - 22363 - 221
115ASNASNASNASNAA65 - 22363 - 221
215ASNASNASNASNEE65 - 22363 - 221
116ASNASNASNASNAA65 - 22363 - 221
216ASNASNASNASNFF65 - 22363 - 221
117ASNASNASNASNAA65 - 22363 - 221
217ASNASNASNASNGG65 - 22363 - 221
118ASNASNASNASNAA65 - 22363 - 221
218ASNASNASNASNHH65 - 22363 - 221
119ASNASNASNASNAA65 - 22363 - 221
219ASNASNASNASNII65 - 22363 - 221
120ASNASNASNASNAA65 - 22363 - 221
220ASNASNASNASNJJ65 - 22363 - 221
121ASNASNASNASNAA65 - 22363 - 221
221ASNASNASNASNKK65 - 22363 - 221
122ASNASNASNASNAA65 - 22363 - 221
222ASNASNASNASNLL65 - 22363 - 221
123SERSERPHEPHEBB2 - 612 - 61
223SERSERPHEPHECC2 - 612 - 61
124SERSERPHEPHEBB2 - 612 - 61
224SERSERPHEPHEDD2 - 612 - 61
125SERSERPHEPHEBB2 - 612 - 61
225SERSERPHEPHEEE2 - 612 - 61
126SERSERPHEPHEBB2 - 612 - 61
226SERSERPHEPHEFF2 - 612 - 61
127SERSERPHEPHEBB2 - 612 - 61
227SERSERPHEPHEGG2 - 612 - 61
128SERSERPHEPHEBB2 - 612 - 61
228SERSERPHEPHEHH2 - 612 - 61
129SERSERPHEPHEBB2 - 612 - 61
229SERSERPHEPHEII2 - 612 - 61
130SERSERPHEPHEBB2 - 612 - 61
230SERSERPHEPHEJJ2 - 612 - 61
131SERSERPHEPHEBB2 - 612 - 61
231SERSERPHEPHEKK2 - 612 - 61
132SERSERPHEPHEBB2 - 612 - 61
232SERSERPHEPHELL2 - 612 - 61
133ASNASNASNASNBB65 - 22363 - 221
233ASNASNASNASNCC65 - 22363 - 221
134ASNASNASNASNBB65 - 22363 - 221
234ASNASNASNASNDD65 - 22363 - 221
135ASNASNASNASNBB65 - 22363 - 221
235ASNASNASNASNEE65 - 22363 - 221
136ASNASNASNASNBB65 - 22363 - 221
236ASNASNASNASNFF65 - 22363 - 221
137ASNASNASNASNBB65 - 22363 - 221
237ASNASNASNASNGG65 - 22363 - 221
138ASNASNASNASNBB65 - 22363 - 221
238ASNASNASNASNHH65 - 22363 - 221
139ASNASNASNASNBB65 - 22363 - 221
239ASNASNASNASNII65 - 22363 - 221
140ASNASNASNASNBB65 - 22363 - 221
240ASNASNASNASNJJ65 - 22363 - 221
141ASNASNASNASNBB65 - 22363 - 221
241ASNASNASNASNKK65 - 22363 - 221
142ASNASNASNASNBB65 - 22363 - 221
242ASNASNASNASNLL65 - 22363 - 221
143SERSERPHEPHECC2 - 612 - 61
243SERSERPHEPHEDD2 - 612 - 61
144SERSERPHEPHECC2 - 612 - 61
244SERSERPHEPHEEE2 - 612 - 61
145SERSERPHEPHECC2 - 612 - 61
245SERSERPHEPHEFF2 - 612 - 61
146SERSERPHEPHECC2 - 612 - 61
246SERSERPHEPHEGG2 - 612 - 61
147SERSERPHEPHECC2 - 612 - 61
247SERSERPHEPHEHH2 - 612 - 61
148SERSERPHEPHECC2 - 612 - 61
248SERSERPHEPHEII2 - 612 - 61
149SERSERPHEPHECC2 - 612 - 61
249SERSERPHEPHEJJ2 - 612 - 61
150SERSERPHEPHECC2 - 612 - 61
250SERSERPHEPHEKK2 - 612 - 61
151SERSERPHEPHECC2 - 612 - 61
251SERSERPHEPHELL2 - 612 - 61
152ASNASNASNASNCC65 - 22363 - 221
252ASNASNASNASNDD65 - 22363 - 221
153ASNASNASNASNCC65 - 22363 - 221
253ASNASNASNASNEE65 - 22363 - 221
154ASNASNASNASNCC65 - 22363 - 221
254ASNASNASNASNFF65 - 22363 - 221
155ASNASNASNASNCC65 - 22363 - 221
255ASNASNASNASNGG65 - 22363 - 221
156ASNASNASNASNCC65 - 22363 - 221
256ASNASNASNASNHH65 - 22363 - 221
157ASNASNASNASNCC65 - 22363 - 221
257ASNASNASNASNII65 - 22363 - 221
158ASNASNASNASNCC65 - 22363 - 221
258ASNASNASNASNJJ65 - 22363 - 221
159ASNASNASNASNCC65 - 22363 - 221
259ASNASNASNASNKK65 - 22363 - 221
160ASNASNASNASNCC65 - 22363 - 221
260ASNASNASNASNLL65 - 22363 - 221
161SERSERPHEPHEDD2 - 612 - 61
261SERSERPHEPHEEE2 - 612 - 61
162SERSERPHEPHEDD2 - 612 - 61
262SERSERPHEPHEFF2 - 612 - 61
163SERSERPHEPHEDD2 - 612 - 61
263SERSERPHEPHEGG2 - 612 - 61
164SERSERPHEPHEDD2 - 612 - 61
264SERSERPHEPHEHH2 - 612 - 61
165SERSERPHEPHEDD2 - 612 - 61
265SERSERPHEPHEII2 - 612 - 61
166SERSERPHEPHEDD2 - 612 - 61
266SERSERPHEPHEJJ2 - 612 - 61
167SERSERPHEPHEDD2 - 612 - 61
267SERSERPHEPHEKK2 - 612 - 61
168SERSERPHEPHEDD2 - 612 - 61
268SERSERPHEPHELL2 - 612 - 61
169ASNASNASNASNDD65 - 22363 - 221
269ASNASNASNASNEE65 - 22363 - 221
170ASNASNASNASNDD65 - 22363 - 221
270ASNASNASNASNFF65 - 22363 - 221
171ASNASNASNASNDD65 - 22363 - 221
271ASNASNASNASNGG65 - 22363 - 221
172ASNASNASNASNDD65 - 22363 - 221
272ASNASNASNASNHH65 - 22363 - 221
173ASNASNASNASNDD65 - 22363 - 221
273ASNASNASNASNII65 - 22363 - 221
174ASNASNASNASNDD65 - 22363 - 221
274ASNASNASNASNJJ65 - 22363 - 221
175ASNASNASNASNDD65 - 22363 - 221
275ASNASNASNASNKK65 - 22363 - 221
176ASNASNASNASNDD65 - 22363 - 221
276ASNASNASNASNLL65 - 22363 - 221
177SERSERPHEPHEEE2 - 612 - 61
277SERSERPHEPHEFF2 - 612 - 61
178SERSERPHEPHEEE2 - 612 - 61
278SERSERPHEPHEGG2 - 612 - 61
179SERSERPHEPHEEE2 - 612 - 61
279SERSERPHEPHEHH2 - 612 - 61
180SERSERPHEPHEEE2 - 612 - 61
280SERSERPHEPHEII2 - 612 - 61
181SERSERPHEPHEEE2 - 612 - 61
281SERSERPHEPHEJJ2 - 612 - 61
182SERSERPHEPHEEE2 - 612 - 61
282SERSERPHEPHEKK2 - 612 - 61
183SERSERPHEPHEEE2 - 612 - 61
283SERSERPHEPHELL2 - 612 - 61
184ASNASNASNASNEE65 - 22363 - 221
284ASNASNASNASNFF65 - 22363 - 221
185ASNASNASNASNEE65 - 22363 - 221
285ASNASNASNASNGG65 - 22363 - 221
186ASNASNASNASNEE65 - 22363 - 221
286ASNASNASNASNHH65 - 22363 - 221
187ASNASNASNASNEE65 - 22363 - 221
287ASNASNASNASNII65 - 22363 - 221
188ASNASNASNASNEE65 - 22363 - 221
288ASNASNASNASNJJ65 - 22363 - 221
189ASNASNASNASNEE65 - 22363 - 221
289ASNASNASNASNKK65 - 22363 - 221
190ASNASNASNASNEE65 - 22363 - 221
290ASNASNASNASNLL65 - 22363 - 221
191SERSERPHEPHEFF2 - 612 - 61
291SERSERPHEPHEGG2 - 612 - 61
192SERSERPHEPHEFF2 - 612 - 61
292SERSERPHEPHEHH2 - 612 - 61
193SERSERPHEPHEFF2 - 612 - 61
293SERSERPHEPHEII2 - 612 - 61
194SERSERPHEPHEFF2 - 612 - 61
294SERSERPHEPHEJJ2 - 612 - 61
195SERSERPHEPHEFF2 - 612 - 61
295SERSERPHEPHEKK2 - 612 - 61
196SERSERPHEPHEFF2 - 612 - 61
296SERSERPHEPHELL2 - 612 - 61
197ASNASNASNASNFF65 - 22363 - 221
297ASNASNASNASNGG65 - 22363 - 221
198ASNASNASNASNFF65 - 22363 - 221
298ASNASNASNASNHH65 - 22363 - 221
199ASNASNASNASNFF65 - 22363 - 221
299ASNASNASNASNII65 - 22363 - 221
1100ASNASNASNASNFF65 - 22363 - 221
2100ASNASNASNASNJJ65 - 22363 - 221
1101ASNASNASNASNFF65 - 22363 - 221
2101ASNASNASNASNKK65 - 22363 - 221
1102ASNASNASNASNFF65 - 22363 - 221
2102ASNASNASNASNLL65 - 22363 - 221
1103SERSERPHEPHEGG2 - 612 - 61
2103SERSERPHEPHEHH2 - 612 - 61
1104SERSERPHEPHEGG2 - 612 - 61
2104SERSERPHEPHEII2 - 612 - 61
1105SERSERPHEPHEGG2 - 612 - 61
2105SERSERPHEPHEJJ2 - 612 - 61
1106SERSERPHEPHEGG2 - 612 - 61
2106SERSERPHEPHEKK2 - 612 - 61
1107SERSERPHEPHEGG2 - 612 - 61
2107SERSERPHEPHELL2 - 612 - 61
1108ASNASNASNASNGG65 - 22363 - 221
2108ASNASNASNASNHH65 - 22363 - 221
1109ASNASNASNASNGG65 - 22363 - 221
2109ASNASNASNASNII65 - 22363 - 221
1110ASNASNASNASNGG65 - 22363 - 221
2110ASNASNASNASNJJ65 - 22363 - 221
1111ASNASNASNASNGG65 - 22363 - 221
2111ASNASNASNASNKK65 - 22363 - 221
1112ASNASNASNASNGG65 - 22363 - 221
2112ASNASNASNASNLL65 - 22363 - 221
1113SERSERPHEPHEHH2 - 612 - 61
2113SERSERPHEPHEII2 - 612 - 61
1114SERSERPHEPHEHH2 - 612 - 61
2114SERSERPHEPHEJJ2 - 612 - 61
1115SERSERPHEPHEHH2 - 612 - 61
2115SERSERPHEPHEKK2 - 612 - 61
1116SERSERPHEPHEHH2 - 612 - 61
2116SERSERPHEPHELL2 - 612 - 61
1117ASNASNASNASNHH65 - 22363 - 221
2117ASNASNASNASNII65 - 22363 - 221
1118ASNASNASNASNHH65 - 22363 - 221
2118ASNASNASNASNJJ65 - 22363 - 221
1119ASNASNASNASNHH65 - 22363 - 221
2119ASNASNASNASNKK65 - 22363 - 221
1120ASNASNASNASNHH65 - 22363 - 221
2120ASNASNASNASNLL65 - 22363 - 221
1121SERSERPHEPHEII2 - 612 - 61
2121SERSERPHEPHEJJ2 - 612 - 61
1122SERSERPHEPHEII2 - 612 - 61
2122SERSERPHEPHEKK2 - 612 - 61
1123SERSERPHEPHEII2 - 612 - 61
2123SERSERPHEPHELL2 - 612 - 61
1124ASNASNASNASNII65 - 22363 - 221
2124ASNASNASNASNJJ65 - 22363 - 221
1125ASNASNASNASNII65 - 22363 - 221
2125ASNASNASNASNKK65 - 22363 - 221
1126ASNASNASNASNII65 - 22363 - 221
2126ASNASNASNASNLL65 - 22363 - 221
1127SERSERPHEPHEJJ2 - 612 - 61
2127SERSERPHEPHEKK2 - 612 - 61
1128SERSERPHEPHEJJ2 - 612 - 61
2128SERSERPHEPHELL2 - 612 - 61
1129ASNASNASNASNJJ65 - 22363 - 221
2129ASNASNASNASNKK65 - 22363 - 221
1130ASNASNASNASNJJ65 - 22363 - 221
2130ASNASNASNASNLL65 - 22363 - 221
1131SERSERPHEPHEKK2 - 612 - 61
2131SERSERPHEPHELL2 - 612 - 61
1132ASNASNASNASNKK65 - 22363 - 221
2132ASNASNASNASNLL65 - 22363 - 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
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
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Components

#1: Protein
Green to red photoconvertible GFP-like protein EosFP


Mass: 25893.434 Da / Num. of mol.: 12 / Mutation: A69T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.2 M chloride hexahydrate, 0.1 M Tris, 30% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 2.7→95.45 Å / Num. obs: 67723 / % possible obs: 95.42 % / Redundancy: 1.7 % / Biso Wilson estimate: 35.46 Å2 / Rsym value: 0.101 / Net I/σ(I): 6.9
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.8 / % possible all: 95.48

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S05
Resolution: 2.7→95.45 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.972 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23151 3344 4.9 %RANDOM
Rwork0.21088 ---
obs0.21189 64379 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.06 Å2-0.01 Å2
2---0.09 Å20.01 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→95.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21444 0 0 471 21915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01922056
X-RAY DIFFRACTIONr_bond_other_d0.0040.0220412
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.96329688
X-RAY DIFFRACTIONr_angle_other_deg0.968347172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33552604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31524.1571068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77153756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7261596
X-RAY DIFFRACTIONr_chiral_restr0.0640.23000
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02124816
X-RAY DIFFRACTIONr_gen_planes_other0.0080.025280
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1143.4310512
X-RAY DIFFRACTIONr_mcbond_other2.1133.42910511
X-RAY DIFFRACTIONr_mcangle_it3.4075.13913068
X-RAY DIFFRACTIONr_mcangle_other3.4085.13913069
X-RAY DIFFRACTIONr_scbond_it2.4143.64411544
X-RAY DIFFRACTIONr_scbond_other2.4143.64511545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9415.35816621
X-RAY DIFFRACTIONr_long_range_B_refined6.23726.59623250
X-RAY DIFFRACTIONr_long_range_B_other6.22626.60523185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29490.14
12B29490.14
21A29050.17
22C29050.17
31A29250.16
32D29250.16
41A29160.15
42E29160.15
51A28750.15
52F28750.15
61A29210.15
62G29210.15
71A29760.15
72H29760.15
81A29150.16
82I29150.16
91A29610.14
92J29610.14
101A29450.15
102K29450.15
111A28830.16
112L28830.16
121A86410.11
122B86410.11
131A87270.11
132C87270.11
141A85150.13
142D85150.13
151A86010.11
152E86010.11
161A85430.12
162F85430.12
171A84720.12
172G84720.12
181A85280.12
182H85280.12
191A85890.12
192I85890.12
201A85180.12
202J85180.12
211A84880.13
212K84880.13
221A87300.11
222L87300.11
231B29790.15
232C29790.15
241B30210.14
242D30210.14
251B31500.09
252E31500.09
261B30070.14
262F30070.14
271B29770.14
272G29770.14
281B30280.12
282H30280.12
291B29930.14
292I29930.14
301B30340.13
302J30340.13
311B29570.14
312K29570.14
321B29860.12
322L29860.12
331B86380.12
332C86380.12
341B86260.13
342D86260.13
351B86000.12
352E86000.12
361B85260.12
362F85260.12
371B84560.13
372G84560.13
381B86260.12
382H86260.12
391B85310.12
392I85310.12
401B84820.13
402J84820.13
411B85370.12
412K85370.12
421B87020.11
422L87020.11
431C29760.13
432D29760.13
441C29490.14
442E29490.14
451C29280.16
452F29280.16
461C29490.16
462G29490.16
471C29750.15
472H29750.15
481C30420.14
482I30420.14
491C29960.14
492J29960.14
501C29420.15
502K29420.15
511C29250.15
512L29250.15
521C85460.13
522D85460.13
531C86780.11
532E86780.11
541C86070.12
542F86070.12
551C85170.12
552G85170.12
561C86430.12
562H86430.12
571C85810.12
572I85810.12
581C85550.12
582J85550.12
591C84450.13
592K84450.13
601C87170.11
602L87170.11
611D30160.13
612E30160.13
621D29630.14
622F29630.14
631D29680.16
632G29680.16
641D30360.13
642H30360.13
651D29770.14
652I29770.14
661D30120.14
662J30120.14
671D30070.13
672K30070.13
681D29730.15
682L29730.15
691D85550.12
692E85550.12
701D84100.13
702F84100.13
711D85160.12
712G85160.12
721D84620.13
722H84620.13
731D84910.13
732I84910.13
741D84010.14
742J84010.14
751D83220.14
752K83220.14
761D86000.12
762L86000.12
771E30060.14
772F30060.14
781E29730.14
782G29730.14
791E30290.11
792H30290.11
801E29590.14
802I29590.14
811E30060.13
812J30060.13
821E29400.14
822K29400.14
831E29740.13
832L29740.13
841E85750.12
842F85750.12
851E86330.12
852G86330.12
861E85640.12
862H85640.12
871E85770.12
872I85770.12
881E85830.12
882J85830.12
891E84350.13
892K84350.13
901E85780.11
902L85780.11
911F29260.13
912G29260.13
921F29440.14
922H29440.14
931F28780.16
932I28780.16
941F29470.14
942J29470.14
951F28830.15
952K28830.15
961F28650.16
962L28650.16
971F84720.13
972G84720.13
981F85060.12
982H85060.12
991F85500.12
992I85500.12
1001F84460.13
1002J84460.13
1011F85670.13
1012K85670.13
1021F85200.12
1022L85200.12
1031G30670.12
1032H30670.12
1041G29880.14
1042I29880.14
1051G29680.14
1052J29680.14
1061G29780.15
1062K29780.15
1071G29810.14
1072L29810.14
1081G84040.13
1082H84040.13
1091G85890.12
1092I85890.12
1101G83620.14
1102J83620.14
1111G84370.14
1112K84370.14
1121G84090.13
1122L84090.13
1131H29610.15
1132I29610.15
1141H30390.11
1142J30390.11
1151H30410.13
1152K30410.13
1161H30580.13
1162L30580.13
1171H84730.12
1172I84730.12
1181H85030.13
1182J85030.13
1191H83460.14
1192K83460.14
1201H85760.12
1202L85760.12
1211I29510.15
1212J29510.15
1221I29450.15
1222K29450.15
1231I29160.16
1232L29160.16
1241I84260.14
1242J84260.14
1251I85070.13
1252K85070.13
1261I85650.12
1262L85650.12
1271J29900.13
1272K29900.13
1281J30050.14
1282L30050.14
1291J83520.14
1292K83520.14
1301J85120.13
1302L85120.13
1311K30070.13
1312L30070.13
1321K84900.13
1322L84900.13
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 259 -
Rwork0.32 4771 -
obs--95.45 %

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