[English] 日本語
Yorodumi
- PDB-5dst: Crystal structure of human PRMT8 in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dst
TitleCrystal structure of human PRMT8 in complex with SAH
ComponentsProtein arginine N-methyltransferase 8
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of protein binding / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / protein homooligomerization ...protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / peptidyl-arginine methylation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of protein binding / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / protein homooligomerization / cytoplasmic side of plasma membrane / enzyme binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.963 Å
AuthorsToma-Fukai, S. / Shimizu, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Novel helical assembly in arginine methyltransferase 8
Authors: Toma-Fukai, S. / Kim, J.D. / Park, K.E. / Kuwabara, N. / Shimizu, N. / Krayukhina, E. / Uchiyama, S. / Fukamizu, A. / Shimizu, T.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Protein arginine N-methyltransferase 8
B: Protein arginine N-methyltransferase 8
C: Protein arginine N-methyltransferase 8
D: Protein arginine N-methyltransferase 8
E: Protein arginine N-methyltransferase 8
F: Protein arginine N-methyltransferase 8
G: Protein arginine N-methyltransferase 8
H: Protein arginine N-methyltransferase 8
I: Protein arginine N-methyltransferase 8
J: Protein arginine N-methyltransferase 8
K: Protein arginine N-methyltransferase 8
L: Protein arginine N-methyltransferase 8
M: Protein arginine N-methyltransferase 8
N: Protein arginine N-methyltransferase 8
O: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)583,44830
Polymers577,68115
Non-polymers5,76615
Water0
1
A: Protein arginine N-methyltransferase 8
B: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-33 kcal/mol
Surface area26800 Å2
MethodPISA
2
C: Protein arginine N-methyltransferase 8
D: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-33 kcal/mol
Surface area26900 Å2
MethodPISA
3
E: Protein arginine N-methyltransferase 8
F: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-33 kcal/mol
Surface area26890 Å2
MethodPISA
4
G: Protein arginine N-methyltransferase 8
H: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-33 kcal/mol
Surface area26850 Å2
MethodPISA
5
I: Protein arginine N-methyltransferase 8
J: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-33 kcal/mol
Surface area26920 Å2
MethodPISA
6
K: Protein arginine N-methyltransferase 8
L: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-33 kcal/mol
Surface area26820 Å2
MethodPISA
7
M: Protein arginine N-methyltransferase 8
N: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-33 kcal/mol
Surface area26850 Å2
MethodPISA
8
O: Protein arginine N-methyltransferase 8
hetero molecules

O: Protein arginine N-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7934
Polymers77,0242
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3260 Å2
ΔGint-33 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.983, 130.943, 294.377
Angle α, β, γ (deg.)90.00, 106.48, 90.00
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
115B
215C
116B
216D
117B
217E
118B
218F
119B
219G
120B
220H
121B
221I
122B
222J
123B
223K
124B
224L
125B
225M
126B
226N
127B
227O
128C
228D
129C
229E
130C
230F
131C
231G
132C
232H
133C
233I
134C
234J
135C
235K
136C
236L
137C
237M
138C
238N
139C
239O
140D
240E
141D
241F
142D
242G
143D
243H
144D
244I
145D
245J
146D
246K
147D
247L
148D
248M
149D
249N
150D
250O
151E
251F
152E
252G
153E
253H
154E
254I
155E
255J
156E
256K
157E
257L
158E
258M
159E
259N
160E
260O
161F
261G
162F
262H
163F
263I
164F
264J
165F
265K
166F
266L
167F
267M
168F
268N
169F
269O
170G
270H
171G
271I
172G
272J
173G
273K
174G
274L
175G
275M
176G
276N
177G
277O
178H
278I
179H
279J
180H
280K
181H
281L
182H
282M
183H
283N
184H
284O
185I
285J
186I
286K
187I
287L
188I
288M
189I
289N
190I
290O
191J
291K
192J
292L
193J
293M
194J
294N
195J
295O
196K
296L
197K
297M
198K
298N
199K
299O
1100L
2100M
1101L
2101N
1102L
2102O
1103M
2103N
1104M
2104O
1105N
2105O

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA79 - 39417 - 332
21SERSERARGARGBB79 - 39417 - 332
12SERSERMETMETAA79 - 39317 - 331
22SERSERMETMETCC79 - 39317 - 331
13SERSERARGARGAA79 - 39417 - 332
23SERSERARGARGDD79 - 39417 - 332
14SERSERARGARGAA79 - 39417 - 332
24SERSERARGARGEE79 - 39417 - 332
15SERSERMETMETAA79 - 39317 - 331
25SERSERMETMETFF79 - 39317 - 331
16SERSERARGARGAA79 - 39417 - 332
26SERSERARGARGGG79 - 39417 - 332
17SERSERMETMETAA79 - 39317 - 331
27SERSERMETMETHH79 - 39317 - 331
18SERSERMETMETAA79 - 39317 - 331
28SERSERMETMETII79 - 39317 - 331
19SERSERARGARGAA79 - 39417 - 332
29SERSERARGARGJJ79 - 39417 - 332
110SERSERARGARGAA79 - 39417 - 332
210SERSERARGARGKK79 - 39417 - 332
111SERSERARGARGAA79 - 39417 - 332
211SERSERARGARGLL79 - 39417 - 332
112SERSERARGARGAA79 - 39417 - 332
212SERSERARGARGMM79 - 39417 - 332
113SERSERARGARGAA79 - 39417 - 332
213SERSERARGARGNN79 - 39417 - 332
114SERSERARGARGAA79 - 39417 - 332
214SERSERARGARGOO79 - 39417 - 332
115SERSERMETMETBB79 - 39317 - 331
215SERSERMETMETCC79 - 39317 - 331
116SERSERARGARGBB79 - 39417 - 332
216SERSERARGARGDD79 - 39417 - 332
117SERSERARGARGBB79 - 39417 - 332
217SERSERARGARGEE79 - 39417 - 332
118SERSERMETMETBB79 - 39317 - 331
218SERSERMETMETFF79 - 39317 - 331
119SERSERARGARGBB79 - 39417 - 332
219SERSERARGARGGG79 - 39417 - 332
120SERSERMETMETBB79 - 39317 - 331
220SERSERMETMETHH79 - 39317 - 331
121SERSERMETMETBB79 - 39317 - 331
221SERSERMETMETII79 - 39317 - 331
122SERSERARGARGBB79 - 39417 - 332
222SERSERARGARGJJ79 - 39417 - 332
123SERSERARGARGBB79 - 39417 - 332
223SERSERARGARGKK79 - 39417 - 332
124SERSERARGARGBB79 - 39417 - 332
224SERSERARGARGLL79 - 39417 - 332
125SERSERARGARGBB79 - 39417 - 332
225SERSERARGARGMM79 - 39417 - 332
126SERSERARGARGBB79 - 39417 - 332
226SERSERARGARGNN79 - 39417 - 332
127SERSERARGARGBB79 - 39417 - 332
227SERSERARGARGOO79 - 39417 - 332
128SERSERMETMETCC79 - 39317 - 331
228SERSERMETMETDD79 - 39317 - 331
129SERSERMETMETCC79 - 39317 - 331
229SERSERMETMETEE79 - 39317 - 331
130ASPASPARGARGCC78 - 39416 - 332
230ASPASPARGARGFF78 - 39416 - 332
131SERSERMETMETCC79 - 39317 - 331
231SERSERMETMETGG79 - 39317 - 331
132ASPASPARGARGCC78 - 39416 - 332
232ASPASPARGARGHH78 - 39416 - 332
133ASPASPARGARGCC78 - 39416 - 332
233ASPASPARGARGII78 - 39416 - 332
134SERSERMETMETCC79 - 39317 - 331
234SERSERMETMETJJ79 - 39317 - 331
135SERSERMETMETCC79 - 39317 - 331
235SERSERMETMETKK79 - 39317 - 331
136SERSERMETMETCC79 - 39317 - 331
236SERSERMETMETLL79 - 39317 - 331
137SERSERMETMETCC79 - 39317 - 331
237SERSERMETMETMM79 - 39317 - 331
138SERSERMETMETCC79 - 39317 - 331
238SERSERMETMETNN79 - 39317 - 331
139SERSERMETMETCC79 - 39317 - 331
239SERSERMETMETOO79 - 39317 - 331
140SERSERARGARGDD79 - 39417 - 332
240SERSERARGARGEE79 - 39417 - 332
141SERSERMETMETDD79 - 39317 - 331
241SERSERMETMETFF79 - 39317 - 331
142SERSERARGARGDD79 - 39417 - 332
242SERSERARGARGGG79 - 39417 - 332
143SERSERMETMETDD79 - 39317 - 331
243SERSERMETMETHH79 - 39317 - 331
144SERSERMETMETDD79 - 39317 - 331
244SERSERMETMETII79 - 39317 - 331
145SERSERARGARGDD79 - 39417 - 332
245SERSERARGARGJJ79 - 39417 - 332
146SERSERARGARGDD79 - 39417 - 332
246SERSERARGARGKK79 - 39417 - 332
147SERSERARGARGDD79 - 39417 - 332
247SERSERARGARGLL79 - 39417 - 332
148SERSERARGARGDD79 - 39417 - 332
248SERSERARGARGMM79 - 39417 - 332
149SERSERARGARGDD79 - 39417 - 332
249SERSERARGARGNN79 - 39417 - 332
150SERSERARGARGDD79 - 39417 - 332
250SERSERARGARGOO79 - 39417 - 332
151SERSERMETMETEE79 - 39317 - 331
251SERSERMETMETFF79 - 39317 - 331
152SERSERARGARGEE79 - 39417 - 332
252SERSERARGARGGG79 - 39417 - 332
153SERSERMETMETEE79 - 39317 - 331
253SERSERMETMETHH79 - 39317 - 331
154SERSERMETMETEE79 - 39317 - 331
254SERSERMETMETII79 - 39317 - 331
155SERSERARGARGEE79 - 39417 - 332
255SERSERARGARGJJ79 - 39417 - 332
156SERSERARGARGEE79 - 39417 - 332
256SERSERARGARGKK79 - 39417 - 332
157SERSERARGARGEE79 - 39417 - 332
257SERSERARGARGLL79 - 39417 - 332
158SERSERARGARGEE79 - 39417 - 332
258SERSERARGARGMM79 - 39417 - 332
159SERSERARGARGEE79 - 39417 - 332
259SERSERARGARGNN79 - 39417 - 332
160SERSERARGARGEE79 - 39417 - 332
260SERSERARGARGOO79 - 39417 - 332
161SERSERMETMETFF79 - 39317 - 331
261SERSERMETMETGG79 - 39317 - 331
162ASPASPARGARGFF78 - 39416 - 332
262ASPASPARGARGHH78 - 39416 - 332
163ASPASPARGARGFF78 - 39416 - 332
263ASPASPARGARGII78 - 39416 - 332
164SERSERMETMETFF79 - 39317 - 331
264SERSERMETMETJJ79 - 39317 - 331
165SERSERMETMETFF79 - 39317 - 331
265SERSERMETMETKK79 - 39317 - 331
166SERSERMETMETFF79 - 39317 - 331
266SERSERMETMETLL79 - 39317 - 331
167SERSERMETMETFF79 - 39317 - 331
267SERSERMETMETMM79 - 39317 - 331
168SERSERMETMETFF79 - 39317 - 331
268SERSERMETMETNN79 - 39317 - 331
169SERSERMETMETFF79 - 39317 - 331
269SERSERMETMETOO79 - 39317 - 331
170SERSERMETMETGG79 - 39317 - 331
270SERSERMETMETHH79 - 39317 - 331
171SERSERMETMETGG79 - 39317 - 331
271SERSERMETMETII79 - 39317 - 331
172SERSERARGARGGG79 - 39417 - 332
272SERSERARGARGJJ79 - 39417 - 332
173SERSERARGARGGG79 - 39417 - 332
273SERSERARGARGKK79 - 39417 - 332
174SERSERARGARGGG79 - 39417 - 332
274SERSERARGARGLL79 - 39417 - 332
175SERSERARGARGGG79 - 39417 - 332
275SERSERARGARGMM79 - 39417 - 332
176SERSERARGARGGG79 - 39417 - 332
276SERSERARGARGNN79 - 39417 - 332
177SERSERARGARGGG79 - 39417 - 332
277SERSERARGARGOO79 - 39417 - 332
178ASPASPARGARGHH78 - 39416 - 332
278ASPASPARGARGII78 - 39416 - 332
179SERSERMETMETHH79 - 39317 - 331
279SERSERMETMETJJ79 - 39317 - 331
180SERSERMETMETHH79 - 39317 - 331
280SERSERMETMETKK79 - 39317 - 331
181SERSERMETMETHH79 - 39317 - 331
281SERSERMETMETLL79 - 39317 - 331
182SERSERMETMETHH79 - 39317 - 331
282SERSERMETMETMM79 - 39317 - 331
183SERSERMETMETHH79 - 39317 - 331
283SERSERMETMETNN79 - 39317 - 331
184SERSERMETMETHH79 - 39317 - 331
284SERSERMETMETOO79 - 39317 - 331
185SERSERMETMETII79 - 39317 - 331
285SERSERMETMETJJ79 - 39317 - 331
186SERSERMETMETII79 - 39317 - 331
286SERSERMETMETKK79 - 39317 - 331
187SERSERMETMETII79 - 39317 - 331
287SERSERMETMETLL79 - 39317 - 331
188SERSERMETMETII79 - 39317 - 331
288SERSERMETMETMM79 - 39317 - 331
189SERSERMETMETII79 - 39317 - 331
289SERSERMETMETNN79 - 39317 - 331
190SERSERMETMETII79 - 39317 - 331
290SERSERMETMETOO79 - 39317 - 331
191SERSERARGARGJJ79 - 39417 - 332
291SERSERARGARGKK79 - 39417 - 332
192SERSERARGARGJJ79 - 39417 - 332
292SERSERARGARGLL79 - 39417 - 332
193SERSERARGARGJJ79 - 39417 - 332
293SERSERARGARGMM79 - 39417 - 332
194SERSERARGARGJJ79 - 39417 - 332
294SERSERARGARGNN79 - 39417 - 332
195SERSERARGARGJJ79 - 39417 - 332
295SERSERARGARGOO79 - 39417 - 332
196SERSERARGARGKK79 - 39417 - 332
296SERSERARGARGLL79 - 39417 - 332
197SERSERARGARGKK79 - 39417 - 332
297SERSERARGARGMM79 - 39417 - 332
198SERSERARGARGKK79 - 39417 - 332
298SERSERARGARGNN79 - 39417 - 332
199SERSERARGARGKK79 - 39417 - 332
299SERSERARGARGOO79 - 39417 - 332
1100SERSERARGARGLL79 - 39417 - 332
2100SERSERARGARGMM79 - 39417 - 332
1101SERSERARGARGLL79 - 39417 - 332
2101SERSERARGARGNN79 - 39417 - 332
1102SERSERARGARGLL79 - 39417 - 332
2102SERSERARGARGOO79 - 39417 - 332
1103SERSERARGARGMM79 - 39417 - 332
2103SERSERARGARGNN79 - 39417 - 332
1104SERSERARGARGMM79 - 39417 - 332
2104SERSERARGARGOO79 - 39417 - 332
1105SERSERARGARGNN79 - 39417 - 332
2105SERSERARGARGOO79 - 39417 - 332

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.02049, -0.918746, -0.394317), (-0.918246, -0.138717, 0.370921), (-0.395481, 0.36968, -0.840792)-4.24352, -14.82616, 23.846661
3given(1), (1), (1)
4given(0.069868, 0.92259, 0.379402), (-0.924691, -0.082791, 0.371607), (0.374252, -0.376794, 0.847326)5.87181, -14.42253, -24.600229
5given(1), (1), (1)
6given(0.696213, 0.200814, -0.689174), (0.202694, -0.975999, -0.079625), (-0.688623, -0.084255, -0.720208)18.74515, -27.41258, 36.530991
7given(1), (1), (1)
8given(-0.696815, -0.187239, 0.69238), (0.193779, -0.978572, -0.069613), (0.690578, 0.085661, 0.718167)-18.010321, -27.160681, -36.492439
9given(1), (1), (1)
10given(-0.432054, 0.869536, -0.239242), (0.87176, 0.334727, -0.35776), (-0.231004, -0.363133, -0.902647)35.512341, -8.24736, 51.331509
11given(1), (1), (1)
12given(0.404557, -0.878792, 0.253098), (0.878605, 0.296701, -0.374194), (0.253745, 0.373756, 0.892144)-34.642281, -8.33329, -52.117691
13given(1), (1), (1)
14given(-0.919219, -0.393175, -0.021213), (-0.391575, 0.907171, 0.153977), (-0.041296, 0.149845, -0.987847)25.19701, -1.75334, 77.810257
15given(1), (1), (1)
16given(0.923135, 0.383442, 0.028174), (-0.383431, 0.912753, 0.140932), (0.028323, -0.140902, 0.989618)-24.83519, -0.34843, -78.038841
17given(1), (1), (1)
18given(0.299529, -0.795908, -0.52613), (-0.786419, -0.518192, 0.336187), (-0.54021, 0.313061, -0.781131)28.381639, -21.83486, 98.161301
19given(1), (1), (1)
20given(-0.289891, 0.800897, 0.523954), (-0.795947, -0.50575, 0.332694), (0.531444, -0.320594, 0.784083)-27.3995, -21.387159, -98.876244
21given(1), (1), (1)
22given(0.530001, 0.55052, -0.645001), (0.561614, -0.797772, -0.219431), (-0.635364, -0.245943, -0.732)55.9575, -25.118311, 108.295578
23given(1), (1), (1)
24given(-0.538981, -0.545015, 0.642229), (0.534589, -0.810551, -0.239211), (0.650933, 0.214398, 0.72823)-53.945938, -21.4361, -110.570824
25given(1), (1), (1)
26given(-0.724232, 0.681696, -0.103819), (0.6792, 0.679229, -0.278093), (-0.119058, -0.271918, -0.954927)62.06189, -5.52117, 128.585587
27given(1), (1), (1)
28given(0.716426, -0.688024, 0.115574), (0.686236, 0.665093, -0.294504), (0.125758, 0.290301, 0.948636)-61.99247, -4.12018, -128.822357
29given(1), (1), (1)
30given(0.699666, 0.206152, -0.684082), (0.202416, -0.975434, -0.086925), (-0.685197, -0.077651, -0.724207)18.58259, -27.25923, 36.896832
31given(1), (1), (1)
32given(0.071947, 0.925414, 0.372066), (-0.922332, -0.080258, 0.377972), (0.379641, -0.370363, 0.847764)6.06988, -14.68554, -24.398359
33given(1), (1), (1)
34given(-0.436768, 0.868529, -0.234287), (0.868609, 0.339436, -0.360972), (-0.233989, -0.361165, -0.902668)35.471149, -7.94701, 51.58596
35given(1), (1), (1)
36given(-0.700302, -0.181548, 0.690375), (0.19064, -0.979558, -0.064214), (0.68792, 0.086644, 0.720596)-17.72254, -27.281481, -36.34399
37given(1), (1), (1)
38given(-0.915418, -0.402247, -0.014411), (-0.399755, 0.9044, 0.149186), (-0.046977, 0.142328, -0.988704)24.7033, -1.05474, 78.265213
39given(1), (1), (1)
40given(0.394707, -0.884225, 0.249704), (0.883598, 0.290783, -0.367015), (0.251914, 0.365501, 0.896074)-33.946259, -8.91717, -52.13213
41given(1), (1), (1)
42given(0.321997, -0.790262, -0.521348), (-0.784485, -0.530991, 0.320363), (-0.530002, 0.305834, -0.790926)27.42057, -20.751789, 99.15638
43given(1), (1), (1)
44given(0.929631, 0.368327, 0.010999), (-0.365807, 0.918852, 0.147976), (0.044397, -0.141587, 0.98893)-23.622681, -1.52932, -77.947517
45given(1), (1), (1)
46given(0.52664, 0.57478, -0.626322), (0.573211, -0.784183, -0.237668), (-0.627758, -0.233849, -0.742452)55.033588, -23.183849, 109.881561
47given(1), (1), (1)
48given(-0.275286, 0.818536, 0.5042), (-0.799724, -0.486044, 0.352424), (0.533535, -0.306203, 0.788404)-25.180691, -22.66258, -98.559883
49given(1), (1), (1)
50given(-0.73727, 0.670663, -0.081507), (0.661669, 0.692425, -0.287648), (-0.136478, -0.266005, -0.954262)60.24749, -3.11105, 130.163849
51given(1), (1), (1)
52given(-0.561747, -0.53013, 0.63514), (0.527156, -0.821048, -0.21906), (0.63761, 0.211761, 0.740682)-51.325119, -23.488501, -110.757652
53given(1), (1), (1)
54given(-0.694547, -0.711429, -0.107108), (-0.706915, 0.647179, 0.28536), (-0.133696, 0.273912, -0.952417)51.73011, -4.86709, 155.105469
55given(1), (1), (1)
56given(-0.396496, 0.885, -0.244063), (0.885017, 0.29782, -0.357839), (-0.244001, -0.357882, -0.901324)35.789909, -10.08314, 51.855869
57given(1), (1), (1)
58given(0.030561, 0.923858, 0.381514), (-0.919133, -0.124008, 0.37392), (0.392759, -0.36209, 0.845359)5.66024, -16.49741, -23.87034
59given(1), (1), (1)
60given(-0.922755, -0.384657, -0.02371), (-0.383726, 0.911333, 0.149082), (-0.035738, 0.146665, -0.988541)24.77899, -1.78132, 77.881706
61given(1), (1), (1)
62given(-0.689217, -0.195889, 0.697573), (0.204889, -0.976157, -0.071685), (0.694983, 0.093518, 0.712919)-18.75913, -27.513041, -36.424381
63given(1), (1), (1)
64given(0.282409, -0.810218, -0.513608), (-0.800103, -0.494312, 0.339839), (-0.529226, 0.314965, -0.787856)27.9657, -21.800779, 98.811127
65given(1), (1), (1)
66given(0.429652, -0.869953, 0.242034), (0.872741, 0.331263, -0.358593), (0.231782, 0.365303, 0.901571)-35.160099, -9.3573, -51.69899
67given(1), (1), (1)
68given(0.545956, 0.540713, -0.63997), (0.545004, -0.809357, -0.218888), (-0.63632, -0.229283, -0.736564)54.370571, -24.877741, 109.805397
69given(1), (1), (1)
70given(0.914636, 0.403657, 0.022396), (-0.401816, 0.901566, 0.160381), (0.044547, -0.15569, 0.986801)-23.680321, -2.12943, -78.146469
71given(1), (1), (1)
72given(-0.720061, 0.684129, -0.116104), (0.6819, 0.666626, -0.301036), (-0.12855, -0.295936, -0.946518)63.125179, -2.9883, 127.637077
73given(1), (1), (1)
74given(-0.288394, 0.791666, 0.538603), (-0.786795, -0.516505, 0.337898), (0.545694, -0.326323, 0.771836)-29.86681, -22.210529, -98.145958
75given(1), (1), (1)
76given(-0.723222, -0.682204, -0.107463), (-0.679521, 0.675156, 0.287082), (-0.123294, 0.280647, -0.951859)53.022789, -6.62188, 154.427155
77given(1), (1), (1)
78given(-0.537437, -0.55445, 0.635411), (0.556761, -0.799207, -0.226463), (0.633387, 0.232062, 0.73822)-53.271172, -24.189501, -110.230019
79given(1), (1), (1)
80given(-0.921403, -0.387697, -0.026611), (-0.387243, 0.910268, 0.146473), (-0.032564, 0.145265, -0.988857)24.74699, -1.47424, 77.902946
81given(1), (1), (1)
82given(0.034961, 0.9233, 0.382486), (-0.918141, -0.121482, 0.377173), (0.394708, -0.364362, 0.843472)5.36841, -16.584311, -23.74077
83given(1), (1), (1)
84given(0.285011, -0.809064, -0.513988), (-0.797658, -0.497544, 0.34087), (-0.531518, 0.312835, -0.787162)27.74379, -21.87314, 99.119453
85given(1), (1), (1)
86given(-0.690921, -0.193049, 0.696678), (0.201061, -0.976979, -0.07132), (0.694408, 0.090798, 0.71383)-18.73057, -27.22473, -36.2197
87given(1), (1), (1)
88given(0.54549, 0.548999, -0.633278), (0.557225, -0.801974, -0.215264), (-0.626052, -0.235454, -0.743385)54.039051, -25.513611, 110.394623
89given(1), (1), (1)
90given(0.421135, -0.874738, 0.239749), (0.873209, 0.319548, -0.367961), (0.245258, 0.364312, 0.898402)-34.60033, -8.70109, -51.471901
91given(1), (1), (1)
92given(-0.729124, 0.675852, -0.107718), (0.673853, 0.681455, -0.285555), (-0.119588, -0.280791, -0.952289)62.339291, -3.73857, 128.843323
93given(1), (1), (1)
94given(0.920357, 0.390938, 0.010535), (-0.388171, 0.909899, 0.146312), (0.047613, -0.138749, 0.989182)-23.045731, -0.8127, -77.513817
95given(1), (1), (1)
96given(-0.715135, -0.69138, -0.102838), (-0.684839, 0.663586, 0.30108), (-0.139919, 0.285741, -0.948037)51.90094, -8.03615, 155.56456
97given(1), (1), (1)
98given(-0.284564, 0.79953, 0.528938), (-0.798304, -0.503122, 0.331027), (0.530786, -0.328054, 0.781439)-28.796049, -20.423349, -97.894272
99given(1), (1), (1)
100given(0.551283, -0.54411, -0.632481), (-0.536492, -0.811755, 0.230718), (-0.638955, 0.21213, -0.739417)62.376499, -25.01495, 172.876541
101given(1), (1), (1)
102given(0.310487, -0.791821, -0.525944), (-0.791974, -0.521475, 0.317556), (-0.525714, 0.317937, -0.789012)27.01606, -21.005671, 98.813507
103given(1), (1), (1)
104given(0.063586, 0.927957, 0.367224), (-0.913792, -0.093782, 0.395208), (0.401175, -0.360696, 0.841996)4.44715, -16.6483, -24.047701
105given(1), (1), (1)
106given(0.536144, 0.553254, -0.637542), (0.551759, -0.801277, -0.231338), (-0.638836, -0.227739, -0.734863)53.747749, -23.16058, 110.236343
107given(1), (1), (1)
108given(-0.698019, -0.187616, 0.691065), (0.204795, -0.977061, -0.058404), (0.68617, 0.10076, 0.72043)-18.73822, -28.51947, -36.43063
109given(1), (1), (1)
110given(-0.734165, 0.670379, -0.10767), (0.667209, 0.68293, -0.297385), (-0.12583, -0.290168, -0.948667)61.694229, -2.36341, 128.453979
111given(1), (1), (1)
112given(0.414765, -0.877477, 0.240841), (0.878694, 0.317491, -0.356504), (0.236359, 0.359491, 0.902718)-35.41959, -9.23571, -51.7048
113given(1), (1), (1)
114given(-0.699253, -0.708045, -0.098578), (-0.703243, 0.656531, 0.272794), (-0.128431, 0.260076, -0.957009)48.841221, -3.44551, 155.05365
115given(1), (1), (1)
116given(0.928683, 0.370765, 0.009033), (-0.366455, 0.913596, 0.176216), (0.057082, -0.166959, 0.98431)-25.007351, -5.21903, -78.480118
117given(1), (1), (1)
118given(0.554052, -0.531175, -0.640998), (-0.53924, -0.815608, 0.209772), (-0.634229, 0.229427, -0.73832)62.39706, -22.02767, 172.487595
119given(1), (1), (1)
120given(-0.279394, 0.808783, 0.517503), (-0.794901, -0.497149, 0.347815), (0.538583, -0.314187, 0.781803)-28.64864, -22.2208, -98.364723
121given(1), (1), (1)
122given(0.532534, 0.55201, -0.641632), (0.553728, -0.800547, -0.229152), (-0.640151, -0.233259, -0.731982)54.13208, -23.46459, 110.192596
123given(1), (1), (1)
124given(0.065341, 0.926056, 0.371686), (-0.915411, -0.092631, 0.391716), (0.397181, -0.365841, 0.84167)3.99335, -16.400339, -23.749559
125given(1), (1), (1)
126given(-0.73964, 0.662585, -0.117958), (0.664084, 0.690102, -0.287665), (-0.1092, -0.291103, -0.950439)62.84721, -2.85346, 128.387589
127given(1), (1), (1)
128given(-0.690203, -0.180172, 0.700826), (0.193387, -0.979207, -0.061284), (0.697295, 0.093232, 0.710695)-19.58062, -27.756571, -35.70496
129given(1), (1), (1)
130given(-0.691377, -0.712885, -0.117445), (-0.711493, 0.643534, 0.28221), (-0.125603, 0.278674, -0.952137)50.421848, -4.55485, 155.336105
131given(1), (1), (1)
132given(0.407352, -0.876526, 0.25645), (0.879582, 0.300975, -0.368441), (0.245763, 0.375654, 0.89358)-36.695591, -8.56162, -50.2784
133given(1), (1), (1)
134given(0.548556, -0.520654, -0.654222), (-0.526101, -0.82308, 0.213909), (-0.64985, 0.226845, -0.725422)64.550873, -23.40818, 172.261108
135given(1), (1), (1)
136given(0.932516, 0.360397, 0.022981), (-0.359148, 0.918861, 0.163425), (0.037781, -0.16065, 0.986288)-26.935829, -4.05928, -77.063492
137given(1), (1), (1)
138given(0.259653, 0.810023, -0.525778), (0.806986, -0.481049, -0.342587), (-0.530429, -0.335342, -0.778583)87.337517, -17.979481, 184.467056
139given(1), (1), (1)
140given(-0.726392, 0.676012, -0.123948), (0.676192, 0.670687, -0.304866), (-0.122963, -0.305265, -0.944295)62.956841, -2.07477, 128.597412
141given(1), (1), (1)
142given(0.043758, 0.921325, 0.386322), (-0.914429, -0.118808, 0.386917), (0.402375, -0.370195, 0.837287)4.4062, -15.93657, -23.631889
143given(1), (1), (1)
144given(-0.706851, -0.697839, -0.115681), (-0.698461, 0.662698, 0.270154), (-0.111863, 0.271757, -0.955842)51.766602, -3.22326, 155.073853
145given(1), (1), (1)
146given(-0.681749, -0.201696, 0.703233), (0.217225, -0.973702, -0.068681), (0.698593, 0.105937, 0.707634)-20.403851, -27.714149, -34.99757
147given(1), (1), (1)
148given(0.546632, -0.540618, -0.639473), (-0.5366, -0.812414, 0.22813), (-0.642848, 0.218438, -0.734187)62.609211, -24.643471, 172.323029
149given(1), (1), (1)
150given(0.416812, -0.878243, 0.234431), (0.875558, 0.318595, -0.363175), (0.244267, 0.356633, 0.901746)-34.153629, -8.77154, -52.131229
151given(1), (1), (1)
152given(0.273545, 0.803561, -0.528642), (0.79347, -0.499172, -0.348185), (-0.543671, -0.324217, -0.774148)87.445518, -16.60956, 184.636612
153given(1), (1), (1)
154given(0.924675, 0.379673, 0.028716), (-0.378981, 0.910465, 0.16561), (0.036733, -0.164018, 0.985773)-26.826481, -3.38316, -76.93045
155given(1), (1), (1)
156given(-0.699609, -0.704055, -0.121873), (-0.706515, 0.656161, 0.26512), (-0.106691, 0.271586, -0.956482)51.870628, -2.41083, 155.230896
157given(1), (1), (1)
158given(0.054912, 0.921603, 0.38423), (-0.912138, -0.110241, 0.39478), (0.406188, -0.372149, 0.834576)4.09757, -16.41832, -23.264709
159given(1), (1), (1)
160given(0.556209, -0.524933, -0.644264), (-0.52843, -0.821738, 0.213329), (-0.6414, 0.221793, -0.734448)63.329929, -23.61038, 172.630905
161given(1), (1), (1)
162given(-0.680891, -0.183528, 0.709017), (0.205876, -0.977021, -0.055191), (0.702853, 0.108391, 0.703029)-20.38072, -28.716209, -34.36972
163given(1), (1), (1)
164given(0.259243, 0.809529, -0.526741), (0.794431, -0.488891, -0.360368), (-0.549248, -0.325037, -0.769856)88.234459, -14.96939, 184.739395
165given(1), (1), (1)
166given(0.404685, -0.881374, 0.243741), (0.88305, 0.307395, -0.354584), (0.237597, 0.35873, 0.902696)-34.505482, -10.29835, -51.523159
167given(1), (1), (1)
168given(-0.932455, 0.360031, -0.030075), (0.359704, 0.917371, -0.170423), (-0.033768, -0.16973, -0.984912)89.603683, 1.16645, 205.606995
169given(1), (1), (1)
170given(0.562753, -0.527182, -0.636701), (-0.52684, -0.822275, 0.215184), (-0.636984, 0.214344, -0.740478)62.353069, -24.033819, 172.843582
171given(1), (1), (1)
172given(0.052617, 0.92419, 0.37829), (-0.912537, -0.109361, 0.394101), (0.405595, -0.36594, 0.837604)5.11311, -17.250971, -23.658119
173given(1), (1), (1)
174given(0.255958, 0.807151, -0.531971), (0.805369, -0.482418, -0.344462), (-0.534665, -0.340265, -0.773533)89.350807, -17.884991, 183.19075
175given(1), (1), (1)
176given(-0.684114, -0.186263, 0.70519), (0.189568, -0.979023, -0.074689), (0.704309, 0.082586, 0.705073)-19.705891, -25.826969, -35.986389
177given(1), (1), (1)
178given(-0.932359, 0.36117, -0.016219), (0.359022, 0.919669, -0.159097), (-0.042545, -0.154158, -0.98713)88.048012, -0.51434, 206.202118
179given(1), (1), (1)
180given(0.401789, -0.881947, 0.246446), (0.883353, 0.30235, -0.358151), (0.241357, 0.3616, 0.900551)-34.288891, -10.53552, -51.836029
181given(1), (1), (1)
182given(0.252025, 0.810813, -0.528267), (0.809554, -0.475729, -0.343954), (-0.530195, -0.340975, -0.776292)89.381561, -17.51989, 183.410828
183given(1), (1), (1)
184given(0.060318, 0.925141, 0.3748), (-0.911764, -0.101758, 0.397909), (0.406262, -0.36573, 0.837373)5.36755, -17.073839, -23.52854
185given(1), (1), (1)
186given(-0.933492, 0.358365, -0.012914), (0.355742, 0.920922, -0.159216), (-0.045164, -0.153221, -0.987159)87.786491, -0.02746, 206.495926
187given(1), (1), (1)
188given(-0.686748, -0.183079, 0.703463), (0.187194, -0.979665, -0.072215), (0.702379, 0.08209, 0.707054)-19.17675, -25.73525, -36.001091
189given(1), (1), (1)
190given(-0.393013, -0.885949, -0.246241), (-0.886442, 0.293839, 0.357602), (-0.244462, 0.358821, -0.900825)81.617996, -8.30953, 230.808014
191given(1), (1), (1)
192given(-0.938318, 0.344688, -0.027382), (0.344134, 0.923231, -0.170927), (-0.033636, -0.169807, -0.984903)88.905602, 2.2293, 204.873856
193given(1), (1), (1)
194given(0.076675, 0.91709, 0.391238), (-0.910724, -0.095299, 0.40187), (0.405835, -0.387123, 0.827909)1.51944, -17.486441, -23.094749
195given(1), (1), (1)
196given(-0.393931, -0.882756, -0.256048), (-0.885372, 0.289622, 0.363643), (-0.246851, 0.369948, -0.895658)82.32074, -9.29803, 230.501236
197given(1), (1), (1)
198given(-0.687059, -0.175647, 0.705051), (0.186402, -0.980476, -0.062617), (0.702285, 0.088402, 0.706386)-19.63006, -26.837839, -35.860802
199given(1), (1), (1)
200given(-0.399007, -0.880296, -0.256656), (-0.883294, 0.293863, 0.365289), (-0.246141, 0.372456, -0.894813)82.87912, -9.61255, 230.289795
201given(1), (1), (1)
202given(0.073249, 0.915531, 0.395522), (-0.911269, -0.099707, 0.399558), (0.405244, -0.389695, 0.826992)1.3498, -17.263741, -23.089849
203given(1), (1), (1)
204given(0.685205, -0.175576, -0.706872), (-0.183982, -0.980761, 0.065262), (-0.704731, 0.085334, -0.704324)99.935463, -23.36805, 245.040543
205given(1), (1), (1)
206given(0.675945, -0.181314, -0.7143), (-0.181335, -0.980382, 0.077257), (-0.714294, 0.077306, -0.695563)101.656067, -24.85117, 244.857651
207given(1), (1), (1)
208given(0.062572, 0.915352, 0.397763), (-0.919729, -0.101868, 0.379106), (0.387535, -0.389555, 0.835502)1.71394, -13.56303, -22.601629
209given(1), (1), (1)
210given(-0.06774, 0.915457, -0.396673), (0.9203, -0.09621, -0.379199), (-0.385304, -0.390745, -0.835978)121.442307, -13.62213, 258.29541

-
Components

#1: Protein
Protein arginine N-methyltransferase 8 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 4


Mass: 38512.094 Da / Num. of mol.: 15 / Fragment: UNP residues 68-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT8, HRMT1L3, HRMT1L4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NR22, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-Cl, NaCl, PEG6000

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9922 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9922 Å / Relative weight: 1
ReflectionResolution: 2.963→50 Å / Num. obs: 145707 / % possible obs: 99.2 % / Redundancy: 5.4 % / Net I/σ(I): 9.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.963→49.65 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.853 / SU B: 20.515 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 7424 5 %RANDOM
Rwork0.2236 ---
obs0.22542 140423 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.05 Å2
2---0.09 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.963→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39062 0 0 0 39062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01940007
X-RAY DIFFRACTIONr_bond_other_d0.0020.0237771
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.95654089
X-RAY DIFFRACTIONr_angle_other_deg0.899387130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65854729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64224.241849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.994157144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08315165
X-RAY DIFFRACTIONr_chiral_restr0.0830.25959
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0244099
X-RAY DIFFRACTIONr_gen_planes_other0.0030.029214
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_it1.5473.15419006
X-RAY DIFFRACTIONr_mcbond_other1.5473.15419005
X-RAY DIFFRACTIONr_mcangle_it2.5674.72923705
X-RAY DIFFRACTIONr_mcangle_other2.5674.72923706
X-RAY DIFFRACTIONr_scbond_it1.7773.33721000
X-RAY DIFFRACTIONr_scbond_other1.7773.33721000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9884.90930385
X-RAY DIFFRACTIONr_long_range_B_refined4.27324.71244099
X-RAY DIFFRACTIONr_long_range_B_other4.27324.71244100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.070.19
1A2977TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.050.19
1A2977TIGHT POSITIONAL0.060.19
1A2995TIGHT POSITIONAL0.060.19
1A2995TIGHT THERMAL2.981.87
2A2977TIGHT POSITIONAL0.060.19
2A2977TIGHT POSITIONAL0.070.19
2A2995TIGHT POSITIONAL0.060.19
2A2995TIGHT POSITIONAL0.060.19
2A2995TIGHT POSITIONAL0.060.19
2A2995TIGHT POSITIONAL0.060.19
2A2995TIGHT POSITIONAL0.060.19
2A2995TIGHT POSITIONAL0.060.19
2A2977TIGHT POSITIONAL0.060.19
2A2977TIGHT POSITIONAL0.070.19
2A2977TIGHT THERMAL4.661.87
3A3002TIGHT POSITIONAL0.070.19
3A2977TIGHT POSITIONAL0.060.19
3A3002TIGHT POSITIONAL0.060.19
3A3002TIGHT POSITIONAL0.070.19
3A2977TIGHT POSITIONAL0.060.19
3A2977TIGHT POSITIONAL0.060.19
3A2977TIGHT POSITIONAL0.060.19
3A2977TIGHT POSITIONAL0.070.19
3A2977TIGHT POSITIONAL0.060.19
3A2977TIGHT POSITIONAL0.060.19
3A2995TIGHT THERMAL3.051.87
4A2995TIGHT POSITIONAL0.060.19
4A2977TIGHT POSITIONAL0.070.19
4A2995TIGHT POSITIONAL0.060.19
4A2977TIGHT POSITIONAL0.050.19
4A2977TIGHT POSITIONAL0.070.19
4A2995TIGHT POSITIONAL0.060.19
4A2995TIGHT POSITIONAL0.060.19
4A2995TIGHT POSITIONAL0.060.19
4A2995TIGHT POSITIONAL0.070.19
4A2995TIGHT POSITIONAL0.060.19
4A2995TIGHT THERMAL2.781.87
5A2995TIGHT POSITIONAL0.050.19
5A2977TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.070.19
5A2977TIGHT POSITIONAL0.060.19
5A2977TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.060.19
5A2995TIGHT POSITIONAL0.060.19
5A2977TIGHT THERMAL2.891.87
6A2995TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.070.19
6A3002TIGHT POSITIONAL0.070.19
6A3002TIGHT POSITIONAL0.070.19
6A2977TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.060.19
6A2977TIGHT POSITIONAL0.070.19
6A2995TIGHT THERMAL5.031.87
7A2977TIGHT POSITIONAL0.060.19
7A2977TIGHT POSITIONAL0.070.19
7A2995TIGHT POSITIONAL0.070.19
7A2995TIGHT POSITIONAL0.060.19
7A2995TIGHT POSITIONAL0.060.19
7A2995TIGHT POSITIONAL0.070.19
7A2995TIGHT POSITIONAL0.070.19
7A2995TIGHT POSITIONAL0.070.19
7A3002TIGHT POSITIONAL0.070.19
7A2977TIGHT POSITIONAL0.060.19
7A2977TIGHT THERMAL3.071.87
8A2977TIGHT POSITIONAL0.050.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT POSITIONAL0.070.19
8A2977TIGHT POSITIONAL0.050.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT POSITIONAL0.070.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT POSITIONAL0.060.19
8A2977TIGHT THERMAL4.711.87
9A2977TIGHT POSITIONAL0.060.19
9A2995TIGHT POSITIONAL0.060.19
9A2995TIGHT POSITIONAL0.060.19
9A2995TIGHT POSITIONAL0.060.19
9A2995TIGHT POSITIONAL0.050.19
9A2995TIGHT POSITIONAL0.050.19
9A2995TIGHT POSITIONAL0.050.19
9A2995TIGHT POSITIONAL0.070.19
9A2995TIGHT POSITIONAL0.050.19
9A2995TIGHT POSITIONAL0.060.19
9A2995TIGHT THERMAL3.31.87
10A2995TIGHT POSITIONAL0.060.19
10A2995TIGHT POSITIONAL0.050.19
10A2995TIGHT POSITIONAL0.050.19
10A2995TIGHT POSITIONAL0.060.19
10A2995TIGHT POSITIONAL0.060.19
10A2995TIGHT POSITIONAL0.050.19
10A2995TIGHT THERMAL3.211.87
11A2995TIGHT THERMAL2.91.87
12A2995TIGHT THERMAL4.691.87
13A2995TIGHT THERMAL3.121.87
14A2995TIGHT THERMAL3.441.87
15B2977TIGHT THERMAL4.641.87
16B2995TIGHT THERMAL3.181.87
17B2995TIGHT THERMAL2.561.87
18B2977TIGHT THERMAL2.681.87
19B2995TIGHT THERMAL5.121.87
20B2977TIGHT THERMAL3.071.87
21B2977TIGHT THERMAL4.841.87
22B2995TIGHT THERMAL3.161.87
23B2995TIGHT THERMAL3.231.87
24B2995TIGHT THERMAL2.941.87
25B2995TIGHT THERMAL4.731.87
26B2995TIGHT THERMAL3.21.87
27B2995TIGHT THERMAL3.151.87
28C2977TIGHT THERMAL3.641.87
29C2977TIGHT THERMAL4.361.87
30C3002TIGHT THERMAL3.851.87
31C2977TIGHT THERMAL2.571.87
32C3002TIGHT THERMAL3.711.87
33C3002TIGHT THERMAL2.021.87
34C2977TIGHT THERMAL3.31.87
35C2977TIGHT THERMAL3.391.87
36C2977TIGHT THERMAL3.761.87
37C2977TIGHT THERMAL2.271.87
38C2977TIGHT THERMAL3.521.87
39C2977TIGHT THERMAL4.961.87
40D2995TIGHT THERMAL2.941.87
41D2977TIGHT THERMAL2.831.87
42D2995TIGHT THERMAL4.131.87
43D2977TIGHT THERMAL2.371.87
44D2977TIGHT THERMAL3.761.87
45D2995TIGHT THERMAL2.571.87
46D2995TIGHT THERMAL2.831.87
47D2995TIGHT THERMAL2.491.87
48D2995TIGHT THERMAL3.81.87
49D2995TIGHT THERMAL2.661.87
50D2995TIGHT THERMAL3.311.87
51E2977TIGHT THERMAL2.831.87
52E2995TIGHT THERMAL4.81.87
53E2977TIGHT THERMAL2.791.87
54E2977TIGHT THERMAL4.471.87
55E2995TIGHT THERMAL3.131.87
56E2995TIGHT THERMAL2.791.87
57E2995TIGHT THERMAL2.711.87
58E2995TIGHT THERMAL4.491.87
59E2995TIGHT THERMAL2.981.87
60E2995TIGHT THERMAL3.421.87
61F2977TIGHT THERMAL4.181.87
62F3002TIGHT THERMAL2.631.87
63F3002TIGHT THERMAL3.921.87
64F2977TIGHT THERMAL2.51.87
65F2977TIGHT THERMAL2.721.87
66F2977TIGHT THERMAL2.551.87
67F2977TIGHT THERMAL3.861.87
68F2977TIGHT THERMAL2.531.87
69F2977TIGHT THERMAL3.291.87
70G2977TIGHT THERMAL4.061.87
71G2977TIGHT THERMAL2.541.87
72G2995TIGHT THERMAL3.771.87
73G2995TIGHT THERMAL3.581.87
74G2995TIGHT THERMAL4.091.87
75G2995TIGHT THERMAL2.481.87
76G2995TIGHT THERMAL3.851.87
77G2995TIGHT THERMAL5.561.87
78H3002TIGHT THERMAL3.791.87
79H2977TIGHT THERMAL2.561.87
80H2977TIGHT THERMAL2.541.87
81H2977TIGHT THERMAL2.441.87
82H2977TIGHT THERMAL3.811.87
83H2977TIGHT THERMAL2.461.87
84H2977TIGHT THERMAL3.461.87
85I2977TIGHT THERMAL3.351.87
86I2977TIGHT THERMAL3.491.87
87I2977TIGHT THERMAL3.881.87
88I2977TIGHT THERMAL2.171.87
89I2977TIGHT THERMAL3.551.87
90I2977TIGHT THERMAL5.021.87
91J2995TIGHT THERMAL2.811.87
92J2995TIGHT THERMAL2.491.87
93J2995TIGHT THERMAL3.261.87
94J2995TIGHT THERMAL2.131.87
95J2995TIGHT THERMAL3.411.87
96K2995TIGHT THERMAL2.61.87
97K2995TIGHT THERMAL3.481.87
98K2995TIGHT THERMAL2.641.87
99K2995TIGHT THERMAL3.71.87
100L2995TIGHT THERMAL3.781.87
101L2995TIGHT THERMAL2.671.87
102L2995TIGHT THERMAL3.131.87
103M2995TIGHT THERMAL3.611.87
104M2995TIGHT THERMAL4.931.87
105N2995TIGHT THERMAL3.541.87
LS refinement shellResolution: 2.963→3.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 472 -
Rwork0.364 8627 -
obs--81.83 %

+
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://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