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- PDB-2gsy: The 2.6A structure of Infectious Bursal Virus Derived T=1 Particles -

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Basic information

Entry
Database: PDB / ID: 2gsy
TitleThe 2.6A structure of Infectious Bursal Virus Derived T=1 Particles
Componentspolyprotein
KeywordsVIRUS / VIRUS-LIKE CAPSID (PROTEIN-PROTEIN COMPLEX) / icosahedral VIRUS
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarriga, D. / Querol-Audi, J. / Abaitua, F. / Saugar, I. / Pous, J. / Verdaguer, N. / Caston, J.R. / Rodriguez, J.F.
CitationJournal: J.Virol. / Year: 2006
Title: The 2.6-angstrom structure of infectious bursal disease virus-derived t=1 particles reveals new stabilizing elements of the virus capsid.
Authors: Garriga, D. / Querol-Audi, J. / Abaitua, F. / Saugar, I. / Pous, J. / Verdaguer, N. / Caston, J.R. / Rodriguez, J.F.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polyprotein
B: polyprotein
C: polyprotein
D: polyprotein
E: polyprotein
F: polyprotein
G: polyprotein
H: polyprotein
I: polyprotein
J: polyprotein
K: polyprotein
L: polyprotein
M: polyprotein
N: polyprotein
O: polyprotein
P: polyprotein
Q: polyprotein
R: polyprotein
S: polyprotein
T: polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)978,68531
Polymers978,24420
Non-polymers44111
Water2,072115
1
A: polyprotein
B: polyprotein
C: polyprotein
D: polyprotein
E: polyprotein
F: polyprotein
G: polyprotein
H: polyprotein
I: polyprotein
J: polyprotein
K: polyprotein
L: polyprotein
M: polyprotein
N: polyprotein
O: polyprotein
P: polyprotein
Q: polyprotein
R: polyprotein
S: polyprotein
T: polyprotein
hetero molecules

A: polyprotein
B: polyprotein
C: polyprotein
D: polyprotein
E: polyprotein
F: polyprotein
G: polyprotein
H: polyprotein
I: polyprotein
J: polyprotein
K: polyprotein
L: polyprotein
M: polyprotein
N: polyprotein
O: polyprotein
P: polyprotein
Q: polyprotein
R: polyprotein
S: polyprotein
T: polyprotein
hetero molecules

A: polyprotein
B: polyprotein
C: polyprotein
D: polyprotein
E: polyprotein
F: polyprotein
G: polyprotein
H: polyprotein
I: polyprotein
J: polyprotein
K: polyprotein
L: polyprotein
M: polyprotein
N: polyprotein
O: polyprotein
P: polyprotein
Q: polyprotein
R: polyprotein
S: polyprotein
T: polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,936,05693
Polymers2,934,73360
Non-polymers1,32333
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area487130 Å2
ΔGint-1577 kcal/mol
Surface area710170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)326.300, 326.300, 326.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-504-

CA

21T-511-

CA

31D-634-

HOH

41T-626-

HOH

51T-638-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51F
61G
71H
81I
91J
101K
111L
121N
131O
141P
151Q
161T
171A
181B
191C
201D
211F
221G
231H
241I
251J
261K
271L
281N
291O
301P
311Q
321T
12E
22A
32B
42C
52D
62F
72G
82H
92I
102J
112K
122L
132N
142O
152P
162Q
172T
182E
192A
202B
212C
222D
232F
242G
252H
262I
272J
282K
292L
302N
312O
322P
332Q
342T
352E
362A
372B
382C
392D
402F
412G
422H
432I
442J
452K
462L
472N
482O
492P
502Q
512T
522E
532A
542B
552C
562D
572F
582G
592H
602I
612J
622K
632L
642N
652O
662P
672Q
682T
692E
702A
712B
722C
732D
742F
752G
762H
772I
782J
792K
802L
812N
822O
832P
842Q
852T
862E
872A
882B
892C
902D
912F
922G
932H
942I
952J
962K
972L
982N
992O
1002P
1012Q
1022T
13M
23A
33B
43C
53D
63F
73G
83H
93I
103J
113K
123L
133N
143O
153P
163Q
173T
183M
193A
203B
213C
223D
233F
243G
253H
263I
273J
283K
293L
303N
313O
323P
333Q
343T
353M
363A
373B
383C
393D
403F
413G
423H
433I
443J
453K
463L
473N
483O
493P
503Q
513T
523M
533A
543B
553C
563D
573F
583G
593H
603I
613J
623K
633L
643N
653O
663P
673Q
683T
14R
24A
34B
44C
54D
64F
74G
84H
94I
104J
114K
124L
134N
144O
154P
164Q
174T
184R
194A
204B
214C
224D
234F
244G
254H
264I
274J
284K
294L
304N
314O
324P
334Q
344T
354R
364A
374B
384C
394D
404F
414G
424H
434I
444J
454K
464L
474N
484O
494P
504Q
514T
15S
25A
35B
45C
55D
65F
75G
85H
95I
105J
115K
125L
135N
145O
155P
165Q
175T
185S
195A
205B
215C
225D
235F
245G
255H
265I
275J
285K
295L
305N
315O
325P
335Q
345T
355S
365A
375B
385C
395D
405F
415G
425H
435I
445J
455K
465L
475N
485O
495P
505Q
515T
525S
535A
545B
555C
565D
575F
585G
595H
605I
615J
625K
635L
645N
655O
665P
675Q
685T

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLEULEUAA8 - 1068 - 106
211THRTHRLEULEUBB8 - 1068 - 106
311THRTHRLEULEUCC8 - 1068 - 106
411THRTHRLEULEUDD8 - 1068 - 106
511THRTHRLEULEUFF8 - 1068 - 106
611THRTHRLEULEUGG8 - 1068 - 106
711THRTHRLEULEUHH8 - 1068 - 106
811THRTHRLEULEUII8 - 1068 - 106
911THRTHRLEULEUJJ8 - 1068 - 106
1011THRTHRLEULEUKK8 - 1068 - 106
1111THRTHRLEULEULL8 - 1068 - 106
1211THRTHRLEULEUNN8 - 1068 - 106
1311THRTHRLEULEUOO8 - 1068 - 106
1411THRTHRLEULEUPP8 - 1068 - 106
1511THRTHRLEULEUQQ8 - 1068 - 106
1611THRTHRLEULEUTT8 - 1068 - 106
1721ASNASNGLYGLYAA125 - 440125 - 440
1821ASNASNGLYGLYBB125 - 440125 - 440
1921ASNASNGLYGLYCC125 - 440125 - 440
2021ASNASNGLYGLYDD125 - 440125 - 440
2121ASNASNGLYGLYFF125 - 440125 - 440
2221ASNASNGLYGLYGG125 - 440125 - 440
2321ASNASNGLYGLYHH125 - 440125 - 440
2421ASNASNGLYGLYII125 - 440125 - 440
2521ASNASNGLYGLYJJ125 - 440125 - 440
2621ASNASNGLYGLYKK125 - 440125 - 440
2721ASNASNGLYGLYLL125 - 440125 - 440
2821ASNASNGLYGLYNN125 - 440125 - 440
2921ASNASNGLYGLYOO125 - 440125 - 440
3021ASNASNGLYGLYPP125 - 440125 - 440
3121ASNASNGLYGLYQQ125 - 440125 - 440
3221ASNASNGLYGLYTT125 - 440125 - 440
112THRTHRTHRTHREE8 - 738 - 73
212THRTHRTHRTHRAA8 - 738 - 73
312THRTHRTHRTHRBB8 - 738 - 73
412THRTHRTHRTHRCC8 - 738 - 73
512THRTHRTHRTHRDD8 - 738 - 73
612THRTHRTHRTHRFF8 - 738 - 73
712THRTHRTHRTHRGG8 - 738 - 73
812THRTHRTHRTHRHH8 - 738 - 73
912THRTHRTHRTHRII8 - 738 - 73
1012THRTHRTHRTHRJJ8 - 738 - 73
1112THRTHRTHRTHRKK8 - 738 - 73
1212THRTHRTHRTHRLL8 - 738 - 73
1312THRTHRTHRTHRNN8 - 738 - 73
1412THRTHRTHRTHROO8 - 738 - 73
1512THRTHRTHRTHRPP8 - 738 - 73
1612THRTHRTHRTHRQQ8 - 738 - 73
1712THRTHRTHRTHRTT8 - 738 - 73
1822LYSLYSLEULEUEE81 - 10681 - 106
1922LYSLYSLEULEUAA81 - 10681 - 106
2022LYSLYSLEULEUBB81 - 10681 - 106
2122LYSLYSLEULEUCC81 - 10681 - 106
2222LYSLYSLEULEUDD81 - 10681 - 106
2322LYSLYSLEULEUFF81 - 10681 - 106
2422LYSLYSLEULEUGG81 - 10681 - 106
2522LYSLYSLEULEUHH81 - 10681 - 106
2622LYSLYSLEULEUII81 - 10681 - 106
2722LYSLYSLEULEUJJ81 - 10681 - 106
2822LYSLYSLEULEUKK81 - 10681 - 106
2922LYSLYSLEULEULL81 - 10681 - 106
3022LYSLYSLEULEUNN81 - 10681 - 106
3122LYSLYSLEULEUOO81 - 10681 - 106
3222LYSLYSLEULEUPP81 - 10681 - 106
3322LYSLYSLEULEUQQ81 - 10681 - 106
3422LYSLYSLEULEUTT81 - 10681 - 106
3532ASNASNTHRTHREE125 - 250125 - 250
3632ASNASNTHRTHRAA125 - 250125 - 250
3732ASNASNTHRTHRBB125 - 250125 - 250
3832ASNASNTHRTHRCC125 - 250125 - 250
3932ASNASNTHRTHRDD125 - 250125 - 250
4032ASNASNTHRTHRFF125 - 250125 - 250
4132ASNASNTHRTHRGG125 - 250125 - 250
4232ASNASNTHRTHRHH125 - 250125 - 250
4332ASNASNTHRTHRII125 - 250125 - 250
4432ASNASNTHRTHRJJ125 - 250125 - 250
4532ASNASNTHRTHRKK125 - 250125 - 250
4632ASNASNTHRTHRLL125 - 250125 - 250
4732ASNASNTHRTHRNN125 - 250125 - 250
4832ASNASNTHRTHROO125 - 250125 - 250
4932ASNASNTHRTHRPP125 - 250125 - 250
5032ASNASNTHRTHRQQ125 - 250125 - 250
5132ASNASNTHRTHRTT125 - 250125 - 250
5242LEULEUVALVALEE255 - 313255 - 313
5342LEULEUVALVALAA255 - 313255 - 313
5442LEULEUVALVALBB255 - 313255 - 313
5542LEULEUVALVALCC255 - 313255 - 313
5642LEULEUVALVALDD255 - 313255 - 313
5742LEULEUVALVALFF255 - 313255 - 313
5842LEULEUVALVALGG255 - 313255 - 313
5942LEULEUVALVALHH255 - 313255 - 313
6042LEULEUVALVALII255 - 313255 - 313
6142LEULEUVALVALJJ255 - 313255 - 313
6242LEULEUVALVALKK255 - 313255 - 313
6342LEULEUVALVALLL255 - 313255 - 313
6442LEULEUVALVALNN255 - 313255 - 313
6542LEULEUVALVALOO255 - 313255 - 313
6642LEULEUVALVALPP255 - 313255 - 313
6742LEULEUVALVALQQ255 - 313255 - 313
6842LEULEUVALVALTT255 - 313255 - 313
6952SERSERTYRTYREE326 - 354326 - 354
7052SERSERTYRTYRAA326 - 354326 - 354
7152SERSERTYRTYRBB326 - 354326 - 354
7252SERSERTYRTYRCC326 - 354326 - 354
7352SERSERTYRTYRDD326 - 354326 - 354
7452SERSERTYRTYRFF326 - 354326 - 354
7552SERSERTYRTYRGG326 - 354326 - 354
7652SERSERTYRTYRHH326 - 354326 - 354
7752SERSERTYRTYRII326 - 354326 - 354
7852SERSERTYRTYRJJ326 - 354326 - 354
7952SERSERTYRTYRKK326 - 354326 - 354
8052SERSERTYRTYRLL326 - 354326 - 354
8152SERSERTYRTYRNN326 - 354326 - 354
8252SERSERTYRTYROO326 - 354326 - 354
8352SERSERTYRTYRPP326 - 354326 - 354
8452SERSERTYRTYRQQ326 - 354326 - 354
8552SERSERTYRTYRTT326 - 354326 - 354
8662VALVALGLYGLYEE363 - 440363 - 440
8762VALVALGLYGLYAA363 - 440363 - 440
8862VALVALGLYGLYBB363 - 440363 - 440
8962VALVALGLYGLYCC363 - 440363 - 440
9062VALVALGLYGLYDD363 - 440363 - 440
9162VALVALGLYGLYFF363 - 440363 - 440
9262VALVALGLYGLYGG363 - 440363 - 440
9362VALVALGLYGLYHH363 - 440363 - 440
9462VALVALGLYGLYII363 - 440363 - 440
9562VALVALGLYGLYJJ363 - 440363 - 440
9662VALVALGLYGLYKK363 - 440363 - 440
9762VALVALGLYGLYLL363 - 440363 - 440
9862VALVALGLYGLYNN363 - 440363 - 440
9962VALVALGLYGLYOO363 - 440363 - 440
10062VALVALGLYGLYPP363 - 440363 - 440
10162VALVALGLYGLYQQ363 - 440363 - 440
10262VALVALGLYGLYTT363 - 440363 - 440
113THRTHRLEULEUMM8 - 1068 - 106
213THRTHRLEULEUAA8 - 1068 - 106
313THRTHRLEULEUBB8 - 1068 - 106
413THRTHRLEULEUCC8 - 1068 - 106
513THRTHRLEULEUDD8 - 1068 - 106
613THRTHRLEULEUFF8 - 1068 - 106
713THRTHRLEULEUGG8 - 1068 - 106
813THRTHRLEULEUHH8 - 1068 - 106
913THRTHRLEULEUII8 - 1068 - 106
1013THRTHRLEULEUJJ8 - 1068 - 106
1113THRTHRLEULEUKK8 - 1068 - 106
1213THRTHRLEULEULL8 - 1068 - 106
1313THRTHRLEULEUNN8 - 1068 - 106
1413THRTHRLEULEUOO8 - 1068 - 106
1513THRTHRLEULEUPP8 - 1068 - 106
1613THRTHRLEULEUQQ8 - 1068 - 106
1713THRTHRLEULEUTT8 - 1068 - 106
1823ASNASNPHEPHEMM125 - 248125 - 248
1923ASNASNPHEPHEAA125 - 248125 - 248
2023ASNASNPHEPHEBB125 - 248125 - 248
2123ASNASNPHEPHECC125 - 248125 - 248
2223ASNASNPHEPHEDD125 - 248125 - 248
2323ASNASNPHEPHEFF125 - 248125 - 248
2423ASNASNPHEPHEGG125 - 248125 - 248
2523ASNASNPHEPHEHH125 - 248125 - 248
2623ASNASNPHEPHEII125 - 248125 - 248
2723ASNASNPHEPHEJJ125 - 248125 - 248
2823ASNASNPHEPHEKK125 - 248125 - 248
2923ASNASNPHEPHELL125 - 248125 - 248
3023ASNASNPHEPHENN125 - 248125 - 248
3123ASNASNPHEPHEOO125 - 248125 - 248
3223ASNASNPHEPHEPP125 - 248125 - 248
3323ASNASNPHEPHEQQ125 - 248125 - 248
3423ASNASNPHEPHETT125 - 248125 - 248
3533LEULEUTHRTHRMM255 - 314255 - 314
3633LEULEUTHRTHRAA255 - 314255 - 314
3733LEULEUTHRTHRBB255 - 314255 - 314
3833LEULEUTHRTHRCC255 - 314255 - 314
3933LEULEUTHRTHRDD255 - 314255 - 314
4033LEULEUTHRTHRFF255 - 314255 - 314
4133LEULEUTHRTHRGG255 - 314255 - 314
4233LEULEUTHRTHRHH255 - 314255 - 314
4333LEULEUTHRTHRII255 - 314255 - 314
4433LEULEUTHRTHRJJ255 - 314255 - 314
4533LEULEUTHRTHRKK255 - 314255 - 314
4633LEULEUTHRTHRLL255 - 314255 - 314
4733LEULEUTHRTHRNN255 - 314255 - 314
4833LEULEUTHRTHROO255 - 314255 - 314
4933LEULEUTHRTHRPP255 - 314255 - 314
5033LEULEUTHRTHRQQ255 - 314255 - 314
5133LEULEUTHRTHRTT255 - 314255 - 314
5243METMETGLYGLYMM325 - 440325 - 440
5343METMETGLYGLYAA325 - 440325 - 440
5443METMETGLYGLYBB325 - 440325 - 440
5543METMETGLYGLYCC325 - 440325 - 440
5643METMETGLYGLYDD325 - 440325 - 440
5743METMETGLYGLYFF325 - 440325 - 440
5843METMETGLYGLYGG325 - 440325 - 440
5943METMETGLYGLYHH325 - 440325 - 440
6043METMETGLYGLYII325 - 440325 - 440
6143METMETGLYGLYJJ325 - 440325 - 440
6243METMETGLYGLYKK325 - 440325 - 440
6343METMETGLYGLYLL325 - 440325 - 440
6443METMETGLYGLYNN325 - 440325 - 440
6543METMETGLYGLYOO325 - 440325 - 440
6643METMETGLYGLYPP325 - 440325 - 440
6743METMETGLYGLYQQ325 - 440325 - 440
6843METMETGLYGLYTT325 - 440325 - 440
114THRTHRLEULEURR8 - 1068 - 106
214THRTHRLEULEUAA8 - 1068 - 106
314THRTHRLEULEUBB8 - 1068 - 106
414THRTHRLEULEUCC8 - 1068 - 106
514THRTHRLEULEUDD8 - 1068 - 106
614THRTHRLEULEUFF8 - 1068 - 106
714THRTHRLEULEUGG8 - 1068 - 106
814THRTHRLEULEUHH8 - 1068 - 106
914THRTHRLEULEUII8 - 1068 - 106
1014THRTHRLEULEUJJ8 - 1068 - 106
1114THRTHRLEULEUKK8 - 1068 - 106
1214THRTHRLEULEULL8 - 1068 - 106
1314THRTHRLEULEUNN8 - 1068 - 106
1414THRTHRLEULEUOO8 - 1068 - 106
1514THRTHRLEULEUPP8 - 1068 - 106
1614THRTHRLEULEUQQ8 - 1068 - 106
1714THRTHRLEULEUTT8 - 1068 - 106
1824ASNASNARGARGRR125 - 202125 - 202
1924ASNASNARGARGAA125 - 202125 - 202
2024ASNASNARGARGBB125 - 202125 - 202
2124ASNASNARGARGCC125 - 202125 - 202
2224ASNASNARGARGDD125 - 202125 - 202
2324ASNASNARGARGFF125 - 202125 - 202
2424ASNASNARGARGGG125 - 202125 - 202
2524ASNASNARGARGHH125 - 202125 - 202
2624ASNASNARGARGII125 - 202125 - 202
2724ASNASNARGARGJJ125 - 202125 - 202
2824ASNASNARGARGKK125 - 202125 - 202
2924ASNASNARGARGLL125 - 202125 - 202
3024ASNASNARGARGNN125 - 202125 - 202
3124ASNASNARGARGOO125 - 202125 - 202
3224ASNASNARGARGPP125 - 202125 - 202
3324ASNASNARGARGQQ125 - 202125 - 202
3424ASNASNARGARGTT125 - 202125 - 202
3534GLYGLYGLYGLYRR340 - 440340 - 440
3634GLYGLYGLYGLYAA340 - 440340 - 440
3734GLYGLYGLYGLYBB340 - 440340 - 440
3834GLYGLYGLYGLYCC340 - 440340 - 440
3934GLYGLYGLYGLYDD340 - 440340 - 440
4034GLYGLYGLYGLYFF340 - 440340 - 440
4134GLYGLYGLYGLYGG340 - 440340 - 440
4234GLYGLYGLYGLYHH340 - 440340 - 440
4334GLYGLYGLYGLYII340 - 440340 - 440
4434GLYGLYGLYGLYJJ340 - 440340 - 440
4534GLYGLYGLYGLYKK340 - 440340 - 440
4634GLYGLYGLYGLYLL340 - 440340 - 440
4734GLYGLYGLYGLYNN340 - 440340 - 440
4834GLYGLYGLYGLYOO340 - 440340 - 440
4934GLYGLYGLYGLYPP340 - 440340 - 440
5034GLYGLYGLYGLYQQ340 - 440340 - 440
5134GLYGLYGLYGLYTT340 - 440340 - 440
115THRTHRLEULEUSS8 - 1068 - 106
215THRTHRLEULEUAA8 - 1068 - 106
315THRTHRLEULEUBB8 - 1068 - 106
415THRTHRLEULEUCC8 - 1068 - 106
515THRTHRLEULEUDD8 - 1068 - 106
615THRTHRLEULEUFF8 - 1068 - 106
715THRTHRLEULEUGG8 - 1068 - 106
815THRTHRLEULEUHH8 - 1068 - 106
915THRTHRLEULEUII8 - 1068 - 106
1015THRTHRLEULEUJJ8 - 1068 - 106
1115THRTHRLEULEUKK8 - 1068 - 106
1215THRTHRLEULEULL8 - 1068 - 106
1315THRTHRLEULEUNN8 - 1068 - 106
1415THRTHRLEULEUOO8 - 1068 - 106
1515THRTHRLEULEUPP8 - 1068 - 106
1615THRTHRLEULEUQQ8 - 1068 - 106
1715THRTHRLEULEUTT8 - 1068 - 106
1825ASNASNASPASPSS125 - 213125 - 213
1925ASNASNASPASPAA125 - 213125 - 213
2025ASNASNASPASPBB125 - 213125 - 213
2125ASNASNASPASPCC125 - 213125 - 213
2225ASNASNASPASPDD125 - 213125 - 213
2325ASNASNASPASPFF125 - 213125 - 213
2425ASNASNASPASPGG125 - 213125 - 213
2525ASNASNASPASPHH125 - 213125 - 213
2625ASNASNASPASPII125 - 213125 - 213
2725ASNASNASPASPJJ125 - 213125 - 213
2825ASNASNASPASPKK125 - 213125 - 213
2925ASNASNASPASPLL125 - 213125 - 213
3025ASNASNASPASPNN125 - 213125 - 213
3125ASNASNASPASPOO125 - 213125 - 213
3225ASNASNASPASPPP125 - 213125 - 213
3325ASNASNASPASPQQ125 - 213125 - 213
3425ASNASNASPASPTT125 - 213125 - 213
3535THRTHRVALVALSS228 - 313228 - 313
3635THRTHRVALVALAA228 - 313228 - 313
3735THRTHRVALVALBB228 - 313228 - 313
3835THRTHRVALVALCC228 - 313228 - 313
3935THRTHRVALVALDD228 - 313228 - 313
4035THRTHRVALVALFF228 - 313228 - 313
4135THRTHRVALVALGG228 - 313228 - 313
4235THRTHRVALVALHH228 - 313228 - 313
4335THRTHRVALVALII228 - 313228 - 313
4435THRTHRVALVALJJ228 - 313228 - 313
4535THRTHRVALVALKK228 - 313228 - 313
4635THRTHRVALVALLL228 - 313228 - 313
4735THRTHRVALVALNN228 - 313228 - 313
4835THRTHRVALVALOO228 - 313228 - 313
4935THRTHRVALVALPP228 - 313228 - 313
5035THRTHRVALVALQQ228 - 313228 - 313
5135THRTHRVALVALTT228 - 313228 - 313
5245SERSERGLYGLYSS328 - 440328 - 440
5345SERSERGLYGLYAA328 - 440328 - 440
5445SERSERGLYGLYBB328 - 440328 - 440
5545SERSERGLYGLYCC328 - 440328 - 440
5645SERSERGLYGLYDD328 - 440328 - 440
5745SERSERGLYGLYFF328 - 440328 - 440
5845SERSERGLYGLYGG328 - 440328 - 440
5945SERSERGLYGLYHH328 - 440328 - 440
6045SERSERGLYGLYII328 - 440328 - 440
6145SERSERGLYGLYJJ328 - 440328 - 440
6245SERSERGLYGLYKK328 - 440328 - 440
6345SERSERGLYGLYLL328 - 440328 - 440
6445SERSERGLYGLYNN328 - 440328 - 440
6545SERSERGLYGLYOO328 - 440328 - 440
6645SERSERGLYGLYPP328 - 440328 - 440
6745SERSERGLYGLYQQ328 - 440328 - 440
6845SERSERGLYGLYTT328 - 440328 - 440

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein
polyprotein / pp / vp2


Mass: 48912.223 Da / Num. of mol.: 20 / Fragment: Capsid protein VP2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Genus: Avibirnavirus / Strain: Soroa / Plasmid: pESC-URA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YPH499 / References: UniProt: P61825
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 323420 / Num. obs: 323420 / % possible obs: 89.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.186

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1WCD

1wcd


Resolution: 2.6→19.97 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.872 / SU B: 26.664 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.939 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26698 15643 5 %RANDOM
Rwork0.25409 ---
all0.25475 350422 --
obs0.25475 295435 88.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.042 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64321 0 11 115 64447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02265589
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.97389629
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27358547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80923.9942504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7331510108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.78715360
X-RAY DIFFRACTIONr_chiral_restr0.080.210797
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0249240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.229589
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.246203
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.22349
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.222
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.2707
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.2116
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0510.215
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3031.543047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.535269005
X-RAY DIFFRACTIONr_scbond_it0.977324732
X-RAY DIFFRACTIONr_scangle_it1.5984.520624
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3115tight positional00.05
12B3115tight positional00.05
13C3115tight positional00.05
14D3115tight positional00.05
15F3115tight positional0.010.05
16G3115tight positional00.05
17H3115tight positional00.05
18I3115tight positional00.05
19J3115tight positional00.05
110K3115tight positional00.05
111L3115tight positional00.05
112N3115tight positional00.05
113O3115tight positional00.05
114P3115tight positional00.05
115Q3115tight positional00.05
116T3115tight positional0.010.05
21E2900tight positional0.020.05
22A2900tight positional00.05
23B2900tight positional00.05
24C2900tight positional00.05
25D2900tight positional00.05
26F2900tight positional00.05
27G2900tight positional00.05
28H2900tight positional00.05
29I2900tight positional00.05
210J2900tight positional00.05
211K2900tight positional00.05
212L2900tight positional00.05
213N2900tight positional00.05
214O2900tight positional00.05
215P2900tight positional00.05
216Q2900tight positional00.05
217T2900tight positional00.05
31M3006tight positional0.020.05
32A3006tight positional00.05
33B3006tight positional00.05
34C3006tight positional00.05
35D3006tight positional00.05
36F3006tight positional00.05
37G3006tight positional00.05
38H3006tight positional00.05
39I3006tight positional00.05
310J3006tight positional00.05
311K3006tight positional00.05
312L3006tight positional00.05
313N3006tight positional00.05
314O3006tight positional00.05
315P3006tight positional00.05
316Q3006tight positional00.05
317T3006tight positional00.05
41R2106tight positional0.020.05
42A2106tight positional00.05
43B2106tight positional00.05
44C2106tight positional00.05
45D2106tight positional00.05
46F2106tight positional00.05
47G2106tight positional00.05
48H2106tight positional00.05
49I2106tight positional00.05
410J2106tight positional00.05
411K2106tight positional00.05
412L2106tight positional00.05
413N2106tight positional00.05
414O2106tight positional00.05
415P2106tight positional00.05
416Q2106tight positional00.05
417T2106tight positional00.05
51S2905tight positional0.020.05
52A2905tight positional00.05
53B2905tight positional00.05
54C2905tight positional00.05
55D2905tight positional00.05
56F2905tight positional00.05
57G2905tight positional00.05
58H2905tight positional00.05
59I2905tight positional00.05
510J2905tight positional00.05
511K2905tight positional00.05
512L2905tight positional00.05
513N2905tight positional00.05
514O2905tight positional00.05
515P2905tight positional00.05
516Q2905tight positional00.05
517T2905tight positional00.05
11A3115tight thermal0.010.5
12B3115tight thermal00.5
13C3115tight thermal00.5
14D3115tight thermal00.5
15F3115tight thermal0.010.5
16G3115tight thermal0.010.5
17H3115tight thermal0.010.5
18I3115tight thermal0.010.5
19J3115tight thermal00.5
110K3115tight thermal0.010.5
111L3115tight thermal0.010.5
112N3115tight thermal0.010.5
113O3115tight thermal00.5
114P3115tight thermal0.010.5
115Q3115tight thermal00.5
116T3115tight thermal0.010.5
21E2900tight thermal0.040.5
22A2900tight thermal0.010.5
23B2900tight thermal00.5
24C2900tight thermal0.010.5
25D2900tight thermal00.5
26F2900tight thermal0.010.5
27G2900tight thermal0.010.5
28H2900tight thermal0.010.5
29I2900tight thermal0.010.5
210J2900tight thermal00.5
211K2900tight thermal0.010.5
212L2900tight thermal0.010.5
213N2900tight thermal0.010.5
214O2900tight thermal0.010.5
215P2900tight thermal0.010.5
216Q2900tight thermal0.010.5
217T2900tight thermal0.010.5
31M3006tight thermal0.040.5
32A3006tight thermal0.010.5
33B3006tight thermal00.5
34C3006tight thermal0.010.5
35D3006tight thermal00.5
36F3006tight thermal0.010.5
37G3006tight thermal0.010.5
38H3006tight thermal0.010.5
39I3006tight thermal0.010.5
310J3006tight thermal00.5
311K3006tight thermal0.010.5
312L3006tight thermal0.010.5
313N3006tight thermal0.010.5
314O3006tight thermal0.010.5
315P3006tight thermal0.010.5
316Q3006tight thermal0.010.5
317T3006tight thermal0.010.5
41R2106tight thermal0.040.5
42A2106tight thermal0.010.5
43B2106tight thermal00.5
44C2106tight thermal0.010.5
45D2106tight thermal00.5
46F2106tight thermal0.010.5
47G2106tight thermal0.010.5
48H2106tight thermal0.010.5
49I2106tight thermal0.010.5
410J2106tight thermal00.5
411K2106tight thermal0.010.5
412L2106tight thermal0.010.5
413N2106tight thermal0.010.5
414O2106tight thermal0.010.5
415P2106tight thermal0.010.5
416Q2106tight thermal0.010.5
417T2106tight thermal0.010.5
51S2905tight thermal0.040.5
52A2905tight thermal0.010.5
53B2905tight thermal0.010.5
54C2905tight thermal0.010.5
55D2905tight thermal00.5
56F2905tight thermal0.010.5
57G2905tight thermal0.010.5
58H2905tight thermal0.010.5
59I2905tight thermal0.010.5
510J2905tight thermal0.010.5
511K2905tight thermal0.010.5
512L2905tight thermal0.010.5
513N2905tight thermal0.010.5
514O2905tight thermal0.010.5
515P2905tight thermal0.010.5
516Q2905tight thermal0.010.5
517T2905tight thermal0.010.5
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 544 -
Rwork0.406 10367 -
obs--42.66 %

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