[English] 日本語
Yorodumi
- PDB-2g18: Crystal Structure of Nostoc sp. 7120 phycocyanobilin:ferredoxin o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g18
TitleCrystal Structure of Nostoc sp. 7120 phycocyanobilin:ferredoxin oxidoreductase (PcyA) Apoprotein
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich
Function / homology
Function and homology information


phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding
Similarity search - Function
Phycocyanobilin:ferredoxin oxidoreductase / oxygen-dependent coproporphyrinogen oxidase - #20 / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTu, S.-L. / Lagarias, J.C. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2007
Title: Insight into the radical mechanism of phycocyanobilin-ferredoxin oxidoreductase (PcyA) revealed by X-ray crystallography and biochemical measurements.
Authors: Tu, S.L. / Rockwell, N.C. / Lagarias, J.C. / Fisher, A.J.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phycocyanobilin:ferredoxin oxidoreductase
B: Phycocyanobilin:ferredoxin oxidoreductase
C: Phycocyanobilin:ferredoxin oxidoreductase
D: Phycocyanobilin:ferredoxin oxidoreductase
E: Phycocyanobilin:ferredoxin oxidoreductase
F: Phycocyanobilin:ferredoxin oxidoreductase
G: Phycocyanobilin:ferredoxin oxidoreductase
H: Phycocyanobilin:ferredoxin oxidoreductase
I: Phycocyanobilin:ferredoxin oxidoreductase
J: Phycocyanobilin:ferredoxin oxidoreductase
K: Phycocyanobilin:ferredoxin oxidoreductase
L: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,10813
Polymers345,06812
Non-polymers401
Water3,423190
1
A: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7962
Polymers28,7561
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Phycocyanobilin:ferredoxin oxidoreductase


Theoretical massNumber of molelcules
Total (without water)28,7561
Polymers28,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.501, 141.332, 121.842
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131A
141B
151C
161D
171E
181F
191G
201H
211I
221J
231K
241L
251A
261B
271C
281D
291E
301F
311G
321H
331I
341J
351K
361L
371A
381B
391C
401D
411E
421F
431G
441H
451I
461J
471K
481L
491A
501B
511C
521D
531E
541F
551G
561H
571I
581J
591K
601L
611A
621B
631C
641D
651E
661F
671G
681H
691I
701J
711K
721L
731A
741B
751C
761D
771E
781F
791G
801H
811I
821J
831K
841L
851A
861B
871C
881D
891E
901F
911G
921H
931I
941J
951K
961L
971A
981B
991C
1001D
1011E
1021F
1031G
1041H
1051I
1061J
1071K
1081L
1091A
1101B
1111C
1121D
1131E
1141F
1151G
1161H
1171I
1181J
1191K
1201L
1211A
1221B
1231C
1241D
1251E
1261F
1271G
1281H
1291I
1301J
1311K
1321L
1331A
1341B
1351C
1361D
1371E
1381F
1391G
1401H
1411I
1421J
1431K
1441L
1451A
1461B
1471C
1481D
1491E
1501F
1511G
1521H
1531I
1541J
1551K
1561L
1571A
1581B
1591C
1601D
1611E
1621F
1631G
1641H
1651I
1661J
1671K
1681L
1691A
1701B
1711C
1721D
1731E
1741F
1751G
1761H
1771I
1781J
1791K
1801L
1811A
1821B
1831C
1841D
1851E
1861F
1871G
1881H
1891I
1901J
1911K
1921L
1931A
1941B
1951C
1961D
1971E
1981F
1991G
2001H
2011I
2021J
2031K
2041L
2051A
2061B
2071C
2081D
2091E
2101F
2111G
2121H
2131I
2141J
2151K
2161L
2171A
2181B
2191C
2201D
2211E
2221F
2231G
2241H
2251I
2261J
2271K
2281L
2291A
2301B
2311C
2321D
2331E
2341F
2351G
2361H
2371I
2381J
2391K
2401L
2411A
2421B
2431C
2441D
2451E
2461F
2471G
2481H
2491I
2501J
2511K
2521L
2531A
2541B
2551C
2561D
2571E
2581F
2591G
2601H
2611I
2621J
2631K
2641L
2651A
2661B
2671C
2681D
2691E
2701F
2711G
2721H
2731I
2741J
2751K
2761L
2771A
2781B
2791C
2801D
2811E
2821F
2831G
2841H
2851I
2861J
2871K
2881L
2891A
2901B
2911C
2921D
2931E
2941F
2951G
2961H
2971I
2981J
2991K
3001L
3011A
3021B
3031C
3041D
3051E
3061F
3071G
3081H
3091I
3101J
3111K
3121L
3131A
3141B
3151C
3161D
3171E
3181F
3191G
3201H
3211I
3221J
3231K
3241L
3251A
3261B
3271C
3281D
3291E
3301F
3311G
3321H
3331I
3341J
3351K
3361L
3371A
3381B
3391C
3401D
3411E
3421F
3431G
3441H
3451I
3461J
3471K
3481L
3491A
3501B
3511C
3521D
3531E
3541F
3551G
3561H
3571I
3581J
3591K
3601L
3611A
3621B
3631C
3641D
3651E
3661F
3671G
3681H
3691I
3701J
3711K
3721L
3731A
3741B
3751C
3761D
3771E
3781F
3791G
3801H
3811I
3821J
3831K
3841L
3851A
3861B
3871C
3881D
3891E
3901F
3911G
3921H
3931I
3941J
3951K
3961L
3971A
3981B
3991C
4001D
4011E
4021F
4031G
4041H
4051I
4061J
4071K
4081L
4091A
4101B
4111C
4121D
4131E
4141F
4151G
4161H
4171I
4181J
4191K
4201L
4211A
4221B
4231C
4241D
4251E
4261F
4271G
4281H
4291I
4301J
4311K
4321L
4331A
4341B
4351C
4361D
4371E
4381F
4391G
4401H
4411I
4421J
4431K
4441L
4451A
4461B
4471C
4481D
4491E
4501F
4511G
4521H
4531I
4541J
4551K
4561L
4571A
4581B
4591C
4601D
4611E
4621F
4631G
4641H
4651I
4661J
4671K
4681L

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE1AA8 - 1716 - 25
21SERSERILEILE1BB8 - 1716 - 25
31SERSERILEILE1CC8 - 1716 - 25
41SERSERILEILE1DD8 - 1716 - 25
51SERSERILEILE1EE8 - 1716 - 25
61SERSERILEILE1FF8 - 1716 - 25
71SERSERILEILE1GG8 - 1716 - 25
81SERSERILEILE1HH8 - 1716 - 25
91SERSERILEILE1II8 - 1716 - 25
101SERSERILEILE1JJ8 - 1716 - 25
111SERSERILEILE1KK8 - 1716 - 25
121SERSERILEILE1LL8 - 1716 - 25
132ARGARGGLNGLN3AA18 - 1926 - 27
142ARGARGGLNGLN3BB18 - 1926 - 27
152ARGARGGLNGLN3CC18 - 1926 - 27
162ARGARGGLNGLN3DD18 - 1926 - 27
172ARGARGGLNGLN3EE18 - 1926 - 27
182ARGARGGLNGLN3FF18 - 1926 - 27
192ARGARGGLNGLN3GG18 - 1926 - 27
202ARGARGGLNGLN3HH18 - 1926 - 27
212ARGARGGLNGLN3II18 - 1926 - 27
222ARGARGGLNGLN3JJ18 - 1926 - 27
232ARGARGGLNGLN3KK18 - 1926 - 27
242ARGARGGLNGLN3LL18 - 1926 - 27
253LEULEUGLUGLU1AA20 - 2528 - 33
263LEULEUGLUGLU1BB20 - 2528 - 33
273LEULEUGLUGLU1CC20 - 2528 - 33
283LEULEUGLUGLU1DD20 - 2528 - 33
293LEULEUGLUGLU1EE20 - 2528 - 33
303LEULEUGLUGLU1FF20 - 2528 - 33
313LEULEUGLUGLU1GG20 - 2528 - 33
323LEULEUGLUGLU1HH20 - 2528 - 33
333LEULEUGLUGLU1II20 - 2528 - 33
343LEULEUGLUGLU1JJ20 - 2528 - 33
353LEULEUGLUGLU1KK20 - 2528 - 33
363LEULEUGLUGLU1LL20 - 2528 - 33
374GLUGLUGLUGLU3AA2634
384GLUGLUGLUGLU3BB2634
394GLUGLUGLUGLU3CC2634
404GLUGLUGLUGLU3DD2634
414GLUGLUGLUGLU3EE2634
424GLUGLUGLUGLU3FF2634
434GLUGLUGLUGLU3GG2634
444GLUGLUGLUGLU3HH2634
454GLUGLUGLUGLU3II2634
464GLUGLUGLUGLU3JJ2634
474GLUGLUGLUGLU3KK2634
484GLUGLUGLUGLU3LL2634
495VALVALTRPTRP1AA27 - 2835 - 36
505VALVALTRPTRP1BB27 - 2835 - 36
515VALVALTRPTRP1CC27 - 2835 - 36
525VALVALTRPTRP1DD27 - 2835 - 36
535VALVALTRPTRP1EE27 - 2835 - 36
545VALVALTRPTRP1FF27 - 2835 - 36
555VALVALTRPTRP1GG27 - 2835 - 36
565VALVALTRPTRP1HH27 - 2835 - 36
575VALVALTRPTRP1II27 - 2835 - 36
585VALVALTRPTRP1JJ27 - 2835 - 36
595VALVALTRPTRP1KK27 - 2835 - 36
605VALVALTRPTRP1LL27 - 2835 - 36
616HISHISASPASP3AA29 - 3337 - 41
626HISHISASPASP3BB29 - 3337 - 41
636HISHISASPASP3CC29 - 3337 - 41
646HISHISASPASP3DD29 - 3337 - 41
656HISHISASPASP3EE29 - 3337 - 41
666HISHISASPASP3FF29 - 3337 - 41
676HISHISASPASP3GG29 - 3337 - 41
686HISHISASPASP3HH29 - 3337 - 41
696HISHISASPASP3II29 - 3337 - 41
706HISHISASPASP3JJ29 - 3337 - 41
716HISHISASPASP3KK29 - 3337 - 41
726HISHISASPASP3LL29 - 3337 - 41
737LEULEUPROPRO1AA34 - 3642 - 44
747LEULEUPROPRO1BB34 - 3642 - 44
757LEULEUPROPRO1CC34 - 3642 - 44
767LEULEUPROPRO1DD34 - 3642 - 44
777LEULEUPROPRO1EE34 - 3642 - 44
787LEULEUPROPRO1FF34 - 3642 - 44
797LEULEUPROPRO1GG34 - 3642 - 44
807LEULEUPROPRO1HH34 - 3642 - 44
817LEULEUPROPRO1II34 - 3642 - 44
827LEULEUPROPRO1JJ34 - 3642 - 44
837LEULEUPROPRO1KK34 - 3642 - 44
847LEULEUPROPRO1LL34 - 3642 - 44
858TYRTYRGLUGLU3AA37 - 4245 - 50
868TYRTYRGLUGLU3BB37 - 4245 - 50
878TYRTYRGLUGLU3CC37 - 4245 - 50
888TYRTYRGLUGLU3DD37 - 4245 - 50
898TYRTYRGLUGLU3EE37 - 4245 - 50
908TYRTYRGLUGLU3FF37 - 4245 - 50
918TYRTYRGLUGLU3GG37 - 4245 - 50
928TYRTYRGLUGLU3HH37 - 4245 - 50
938TYRTYRGLUGLU3II37 - 4245 - 50
948TYRTYRGLUGLU3JJ37 - 4245 - 50
958TYRTYRGLUGLU3KK37 - 4245 - 50
968TYRTYRGLUGLU3LL37 - 4245 - 50
979LEULEUILEILE1AA43 - 5751 - 65
989LEULEUILEILE1BB43 - 5751 - 65
999LEULEUILEILE1CC43 - 5751 - 65
1009LEULEUILEILE1DD43 - 5751 - 65
1019LEULEUILEILE1EE43 - 5751 - 65
1029LEULEUILEILE1FF43 - 5751 - 65
1039LEULEUILEILE1GG43 - 5751 - 65
1049LEULEUILEILE1HH43 - 5751 - 65
1059LEULEUILEILE1II43 - 5751 - 65
1069LEULEUILEILE1JJ43 - 5751 - 65
1079LEULEUILEILE1KK43 - 5751 - 65
1089LEULEUILEILE1LL43 - 5751 - 65
10910GLUGLUGLUGLU3AA5866
11010GLUGLUGLUGLU3BB5866
11110GLUGLUGLUGLU3CC5866
11210GLUGLUGLUGLU3DD5866
11310GLUGLUGLUGLU3EE5866
11410GLUGLUGLUGLU3FF5866
11510GLUGLUGLUGLU3GG5866
11610GLUGLUGLUGLU3HH5866
11710GLUGLUGLUGLU3II5866
11810GLUGLUGLUGLU3JJ5866
11910GLUGLUGLUGLU3KK5866
12010GLUGLUGLUGLU3LL5866
12111ASNASNPHEPHE1AA59 - 6767 - 75
12211ASNASNPHEPHE1BB59 - 6767 - 75
12311ASNASNPHEPHE1CC59 - 6767 - 75
12411ASNASNPHEPHE1DD59 - 6767 - 75
12511ASNASNPHEPHE1EE59 - 6767 - 75
12611ASNASNPHEPHE1FF59 - 6767 - 75
12711ASNASNPHEPHE1GG59 - 6767 - 75
12811ASNASNPHEPHE1HH59 - 6767 - 75
12911ASNASNPHEPHE1II59 - 6767 - 75
13011ASNASNPHEPHE1JJ59 - 6767 - 75
13111ASNASNPHEPHE1KK59 - 6767 - 75
13211ASNASNPHEPHE1LL59 - 6767 - 75
13312ARGARGARGARG3AA6876
13412ARGARGARGARG3BB6876
13512ARGARGARGARG3CC6876
13612ARGARGARGARG3DD6876
13712ARGARGARGARG3EE6876
13812ARGARGARGARG3FF6876
13912ARGARGARGARG3GG6876
14012ARGARGARGARG3HH6876
14112ARGARGARGARG3II6876
14212ARGARGARGARG3JJ6876
14312ARGARGARGARG3KK6876
14412ARGARGARGARG3LL6876
14513LYSLYSGLYGLY1AA69 - 7877 - 86
14613LYSLYSGLYGLY1BB69 - 7877 - 86
14713LYSLYSGLYGLY1CC69 - 7877 - 86
14813LYSLYSGLYGLY1DD69 - 7877 - 86
14913LYSLYSGLYGLY1EE69 - 7877 - 86
15013LYSLYSGLYGLY1FF69 - 7877 - 86
15113LYSLYSGLYGLY1GG69 - 7877 - 86
15213LYSLYSGLYGLY1HH69 - 7877 - 86
15313LYSLYSGLYGLY1II69 - 7877 - 86
15413LYSLYSGLYGLY1JJ69 - 7877 - 86
15513LYSLYSGLYGLY1KK69 - 7877 - 86
15613LYSLYSGLYGLY1LL69 - 7877 - 86
15714ASNASNLEULEU3AA79 - 8187 - 89
15814ASNASNLEULEU3BB79 - 8187 - 89
15914ASNASNLEULEU3CC79 - 8187 - 89
16014ASNASNLEULEU3DD79 - 8187 - 89
16114ASNASNLEULEU3EE79 - 8187 - 89
16214ASNASNLEULEU3FF79 - 8187 - 89
16314ASNASNLEULEU3GG79 - 8187 - 89
16414ASNASNLEULEU3HH79 - 8187 - 89
16514ASNASNLEULEU3II79 - 8187 - 89
16614ASNASNLEULEU3JJ79 - 8187 - 89
16714ASNASNLEULEU3KK79 - 8187 - 89
16814ASNASNLEULEU3LL79 - 8187 - 89
16915ASPASPTYRTYR1AA82 - 9490 - 102
17015ASPASPTYRTYR1BB82 - 9490 - 102
17115ASPASPTYRTYR1CC82 - 9490 - 102
17215ASPASPTYRTYR1DD82 - 9490 - 102
17315ASPASPTYRTYR1EE82 - 9490 - 102
17415ASPASPTYRTYR1FF82 - 9490 - 102
17515ASPASPTYRTYR1GG82 - 9490 - 102
17615ASPASPTYRTYR1HH82 - 9490 - 102
17715ASPASPTYRTYR1II82 - 9490 - 102
17815ASPASPTYRTYR1JJ82 - 9490 - 102
17915ASPASPTYRTYR1KK82 - 9490 - 102
18015ASPASPTYRTYR1LL82 - 9490 - 102
18116ASPASPASPASP3AA95103
18216ASPASPASPASP3BB95103
18316ASPASPASPASP3CC95103
18416ASPASPASPASP3DD95103
18516ASPASPASPASP3EE95103
18616ASPASPASPASP3FF95103
18716ASPASPASPASP3GG95103
18816ASPASPASPASP3HH95103
18916ASPASPASPASP3II95103
19016ASPASPASPASP3JJ95103
19116ASPASPASPASP3KK95103
19216ASPASPASPASP3LL95103
19317LEULEUGLYGLY1AA96 - 105104 - 113
19417LEULEUGLYGLY1BB96 - 105104 - 113
19517LEULEUGLYGLY1CC96 - 105104 - 113
19617LEULEUGLYGLY1DD96 - 105104 - 113
19717LEULEUGLYGLY1EE96 - 105104 - 113
19817LEULEUGLYGLY1FF96 - 105104 - 113
19917LEULEUGLYGLY1GG96 - 105104 - 113
20017LEULEUGLYGLY1HH96 - 105104 - 113
20117LEULEUGLYGLY1II96 - 105104 - 113
20217LEULEUGLYGLY1JJ96 - 105104 - 113
20317LEULEUGLYGLY1KK96 - 105104 - 113
20417LEULEUGLYGLY1LL96 - 105104 - 113
20518GLYGLYGLNGLN6AA106 - 109114 - 117
20618GLYGLYGLNGLN6BB106 - 109114 - 117
20718GLYGLYGLNGLN6CC106 - 109114 - 117
20818GLYGLYGLNGLN6DD106 - 109114 - 117
20918GLYGLYGLNGLN6EE106 - 109114 - 117
21018GLYGLYGLNGLN6FF106 - 109114 - 117
21118GLYGLYGLNGLN6GG106 - 109114 - 117
21218GLYGLYGLNGLN6HH106 - 109114 - 117
21318GLYGLYGLNGLN6II106 - 109114 - 117
21418GLYGLYGLNGLN6JJ106 - 109114 - 117
21518GLYGLYGLNGLN6KK106 - 109114 - 117
21618GLYGLYGLNGLN6LL106 - 109114 - 117
21719ILEILEVALVAL1AA110 - 120118 - 128
21819ILEILEVALVAL1BB110 - 120118 - 128
21919ILEILEVALVAL1CC110 - 120118 - 128
22019ILEILEVALVAL1DD110 - 120118 - 128
22119ILEILEVALVAL1EE110 - 120118 - 128
22219ILEILEVALVAL1FF110 - 120118 - 128
22319ILEILEVALVAL1GG110 - 120118 - 128
22419ILEILEVALVAL1HH110 - 120118 - 128
22519ILEILEVALVAL1II110 - 120118 - 128
22619ILEILEVALVAL1JJ110 - 120118 - 128
22719ILEILEVALVAL1KK110 - 120118 - 128
22819ILEILEVALVAL1LL110 - 120118 - 128
22920HISHISLEULEU6AA121 - 126129 - 134
23020HISHISLEULEU6BB121 - 126129 - 134
23120HISHISLEULEU6CC121 - 126129 - 134
23220HISHISLEULEU6DD121 - 126129 - 134
23320HISHISLEULEU6EE121 - 126129 - 134
23420HISHISLEULEU6FF121 - 126129 - 134
23520HISHISLEULEU6GG121 - 126129 - 134
23620HISHISLEULEU6HH121 - 126129 - 134
23720HISHISLEULEU6II121 - 126129 - 134
23820HISHISLEULEU6JJ121 - 126129 - 134
23920HISHISLEULEU6KK121 - 126129 - 134
24020HISHISLEULEU6LL121 - 126129 - 134
24121PROPROPROPRO1AA127135
24221PROPROPROPRO1BB127135
24321PROPROPROPRO1CC127135
24421PROPROPROPRO1DD127135
24521PROPROPROPRO1EE127135
24621PROPROPROPRO1FF127135
24721PROPROPROPRO1GG127135
24821PROPROPROPRO1HH127135
24921PROPROPROPRO1II127135
25021PROPROPROPRO1JJ127135
25121PROPROPROPRO1KK127135
25221PROPROPROPRO1LL127135
25322GLUGLUGLUGLU3AA128136
25422GLUGLUGLUGLU3BB128136
25522GLUGLUGLUGLU3CC128136
25622GLUGLUGLUGLU3DD128136
25722GLUGLUGLUGLU3EE128136
25822GLUGLUGLUGLU3FF128136
25922GLUGLUGLUGLU3GG128136
26022GLUGLUGLUGLU3HH128136
26122GLUGLUGLUGLU3II128136
26222GLUGLUGLUGLU3JJ128136
26322GLUGLUGLUGLU3KK128136
26422GLUGLUGLUGLU3LL128136
26523SERSERLEULEU1AA129 - 134137 - 142
26623SERSERLEULEU1BB129 - 134137 - 142
26723SERSERLEULEU1CC129 - 134137 - 142
26823SERSERLEULEU1DD129 - 134137 - 142
26923SERSERLEULEU1EE129 - 134137 - 142
27023SERSERLEULEU1FF129 - 134137 - 142
27123SERSERLEULEU1GG129 - 134137 - 142
27223SERSERLEULEU1HH129 - 134137 - 142
27323SERSERLEULEU1II129 - 134137 - 142
27423SERSERLEULEU1JJ129 - 134137 - 142
27523SERSERLEULEU1KK129 - 134137 - 142
27623SERSERLEULEU1LL129 - 134137 - 142
27724THRTHRGLNGLN5AA135 - 144143 - 152
27824THRTHRGLNGLN5BB135 - 144143 - 152
27924THRTHRGLNGLN5CC135 - 144143 - 152
28024THRTHRGLNGLN5DD135 - 144143 - 152
28124THRTHRGLNGLN5EE135 - 144143 - 152
28224THRTHRGLNGLN5FF135 - 144143 - 152
28324THRTHRGLNGLN5GG135 - 144143 - 152
28424THRTHRGLNGLN5HH135 - 144143 - 152
28524THRTHRGLNGLN5II135 - 144143 - 152
28624THRTHRGLNGLN5JJ135 - 144143 - 152
28724THRTHRGLNGLN5KK135 - 144143 - 152
28824THRTHRGLNGLN5LL135 - 144143 - 152
28925PROPROLEULEU1AA145 - 148153 - 156
29025PROPROLEULEU1BB145 - 148153 - 156
29125PROPROLEULEU1CC145 - 148153 - 156
29225PROPROLEULEU1DD145 - 148153 - 156
29325PROPROLEULEU1EE145 - 148153 - 156
29425PROPROLEULEU1FF145 - 148153 - 156
29525PROPROLEULEU1GG145 - 148153 - 156
29625PROPROLEULEU1HH145 - 148153 - 156
29725PROPROLEULEU1II145 - 148153 - 156
29825PROPROLEULEU1JJ145 - 148153 - 156
29925PROPROLEULEU1KK145 - 148153 - 156
30025PROPROLEULEU1LL145 - 148153 - 156
30126PROPROASNASN6AA149 - 153157 - 161
30226PROPROASNASN6BB149 - 153157 - 161
30326PROPROASNASN6CC149 - 153157 - 161
30426PROPROASNASN6DD149 - 153157 - 161
30526PROPROASNASN6EE149 - 153157 - 161
30626PROPROASNASN6FF149 - 153157 - 161
30726PROPROASNASN6GG149 - 153157 - 161
30826PROPROASNASN6HH149 - 153157 - 161
30926PROPROASNASN6II149 - 153157 - 161
31026PROPROASNASN6JJ149 - 153157 - 161
31126PROPROASNASN6KK149 - 153157 - 161
31226PROPROASNASN6LL149 - 153157 - 161
31327ILEILESERSER1AA154 - 156162 - 164
31427ILEILESERSER1BB154 - 156162 - 164
31527ILEILESERSER1CC154 - 156162 - 164
31627ILEILESERSER1DD154 - 156162 - 164
31727ILEILESERSER1EE154 - 156162 - 164
31827ILEILESERSER1FF154 - 156162 - 164
31927ILEILESERSER1GG154 - 156162 - 164
32027ILEILESERSER1HH154 - 156162 - 164
32127ILEILESERSER1II154 - 156162 - 164
32227ILEILESERSER1JJ154 - 156162 - 164
32327ILEILESERSER1KK154 - 156162 - 164
32427ILEILESERSER1LL154 - 156162 - 164
32528ASPASPPHEPHE3AA157 - 158165 - 166
32628ASPASPPHEPHE3BB157 - 158165 - 166
32728ASPASPPHEPHE3CC157 - 158165 - 166
32828ASPASPPHEPHE3DD157 - 158165 - 166
32928ASPASPPHEPHE3EE157 - 158165 - 166
33028ASPASPPHEPHE3FF157 - 158165 - 166
33128ASPASPPHEPHE3GG157 - 158165 - 166
33228ASPASPPHEPHE3HH157 - 158165 - 166
33328ASPASPPHEPHE3II157 - 158165 - 166
33428ASPASPPHEPHE3JJ157 - 158165 - 166
33528ASPASPPHEPHE3KK157 - 158165 - 166
33628ASPASPPHEPHE3LL157 - 158165 - 166
33729CYSCYSVALVAL1AA159 - 162167 - 170
33829CYSCYSVALVAL1BB159 - 162167 - 170
33929CYSCYSVALVAL1CC159 - 162167 - 170
34029CYSCYSVALVAL1DD159 - 162167 - 170
34129CYSCYSVALVAL1EE159 - 162167 - 170
34229CYSCYSVALVAL1FF159 - 162167 - 170
34329CYSCYSVALVAL1GG159 - 162167 - 170
34429CYSCYSVALVAL1HH159 - 162167 - 170
34529CYSCYSVALVAL1II159 - 162167 - 170
34629CYSCYSVALVAL1JJ159 - 162167 - 170
34729CYSCYSVALVAL1KK159 - 162167 - 170
34829CYSCYSVALVAL1LL159 - 162167 - 170
34930ARGARGARGARG3AA163171
35030ARGARGARGARG3BB163171
35130ARGARGARGARG3CC163171
35230ARGARGARGARG3DD163171
35330ARGARGARGARG3EE163171
35430ARGARGARGARG3FF163171
35530ARGARGARGARG3GG163171
35630ARGARGARGARG3HH163171
35730ARGARGARGARG3II163171
35830ARGARGARGARG3JJ163171
35930ARGARGARGARG3KK163171
36030ARGARGARGARG3LL163171
36131PROPROPROPRO1AA164 - 167172 - 175
36231PROPROPROPRO1BB164 - 167172 - 175
36331PROPROPROPRO1CC164 - 167172 - 175
36431PROPROPROPRO1DD164 - 167172 - 175
36531PROPROPROPRO1EE164 - 167172 - 175
36631PROPROPROPRO1FF164 - 167172 - 175
36731PROPROPROPRO1GG164 - 167172 - 175
36831PROPROPROPRO1HH164 - 167172 - 175
36931PROPROPROPRO1II164 - 167172 - 175
37031PROPROPROPRO1JJ164 - 167172 - 175
37131PROPROPROPRO1KK164 - 167172 - 175
37231PROPROPROPRO1LL164 - 167172 - 175
37332GLUGLUGLUGLU3AA168176
37432GLUGLUGLUGLU3BB168176
37532GLUGLUGLUGLU3CC168176
37632GLUGLUGLUGLU3DD168176
37732GLUGLUGLUGLU3EE168176
37832GLUGLUGLUGLU3FF168176
37932GLUGLUGLUGLU3GG168176
38032GLUGLUGLUGLU3HH168176
38132GLUGLUGLUGLU3II168176
38232GLUGLUGLUGLU3JJ168176
38332GLUGLUGLUGLU3KK168176
38432GLUGLUGLUGLU3LL168176
38533GLUGLUSERSER1AA169 - 192177 - 200
38633GLUGLUSERSER1BB169 - 192177 - 200
38733GLUGLUSERSER1CC169 - 192177 - 200
38833GLUGLUSERSER1DD169 - 192177 - 200
38933GLUGLUSERSER1EE169 - 192177 - 200
39033GLUGLUSERSER1FF169 - 192177 - 200
39133GLUGLUSERSER1GG169 - 192177 - 200
39233GLUGLUSERSER1HH169 - 192177 - 200
39333GLUGLUSERSER1II169 - 192177 - 200
39433GLUGLUSERSER1JJ169 - 192177 - 200
39533GLUGLUSERSER1KK169 - 192177 - 200
39633GLUGLUSERSER1LL169 - 192177 - 200
39734PROPROLEULEU6AA193 - 203201 - 211
39834PROPROLEULEU6BB193 - 203201 - 211
39934PROPROLEULEU6CC193 - 203201 - 211
40034PROPROLEULEU6DD193 - 203201 - 211
40134PROPROLEULEU6EE193 - 203201 - 211
40234PROPROLEULEU6FF193 - 203201 - 211
40334PROPROLEULEU6GG193 - 203201 - 211
40434PROPROLEULEU6HH193 - 203201 - 211
40534PROPROLEULEU6II193 - 203201 - 211
40634PROPROLEULEU6JJ193 - 203201 - 211
40734PROPROLEULEU6KK193 - 203201 - 211
40834PROPROLEULEU6LL193 - 203201 - 211
40935ALAALAGLNGLN1AA204 - 206212 - 214
41035ALAALAGLNGLN1BB204 - 206212 - 214
41135ALAALAGLNGLN1CC204 - 206212 - 214
41235ALAALAGLNGLN1DD204 - 206212 - 214
41335ALAALAGLNGLN1EE204 - 206212 - 214
41435ALAALAGLNGLN1FF204 - 206212 - 214
41535ALAALAGLNGLN1GG204 - 206212 - 214
41635ALAALAGLNGLN1HH204 - 206212 - 214
41735ALAALAGLNGLN1II204 - 206212 - 214
41835ALAALAGLNGLN1JJ204 - 206212 - 214
41935ALAALAGLNGLN1KK204 - 206212 - 214
42035ALAALAGLNGLN1LL204 - 206212 - 214
42136HISHISHISHIS3AA207215
42236HISHISHISHIS3BB207215
42336HISHISHISHIS3CC207215
42436HISHISHISHIS3DD207215
42536HISHISHISHIS3EE207215
42636HISHISHISHIS3FF207215
42736HISHISHISHIS3GG207215
42836HISHISHISHIS3HH207215
42936HISHISHISHIS3II207215
43036HISHISHISHIS3JJ207215
43136HISHISHISHIS3KK207215
43236HISHISHISHIS3LL207215
43337ASNASNARGARG1AA208 - 220216 - 228
43437ASNASNARGARG1BB208 - 220216 - 228
43537ASNASNARGARG1CC208 - 220216 - 228
43637ASNASNARGARG1DD208 - 220216 - 228
43737ASNASNARGARG1EE208 - 220216 - 228
43837ASNASNARGARG1FF208 - 220216 - 228
43937ASNASNARGARG1GG208 - 220216 - 228
44037ASNASNARGARG1HH208 - 220216 - 228
44137ASNASNARGARG1II208 - 220216 - 228
44237ASNASNARGARG1JJ208 - 220216 - 228
44337ASNASNARGARG1KK208 - 220216 - 228
44437ASNASNARGARG1LL208 - 220216 - 228
44538ARGARGARGARG3AA221229
44638ARGARGARGARG3BB221229
44738ARGARGARGARG3CC221229
44838ARGARGARGARG3DD221229
44938ARGARGARGARG3EE221229
45038ARGARGARGARG3FF221229
45138ARGARGARGARG3GG221229
45238ARGARGARGARG3HH221229
45338ARGARGARGARG3II221229
45438ARGARGARGARG3JJ221229
45538ARGARGARGARG3KK221229
45638ARGARGARGARG3LL221229
45739VALVALLEULEU1AA222 - 243230 - 251
45839VALVALLEULEU1BB222 - 243230 - 251
45939VALVALLEULEU1CC222 - 243230 - 251
46039VALVALLEULEU1DD222 - 243230 - 251
46139VALVALLEULEU1EE222 - 243230 - 251
46239VALVALLEULEU1FF222 - 243230 - 251
46339VALVALLEULEU1GG222 - 243230 - 251
46439VALVALLEULEU1HH222 - 243230 - 251
46539VALVALLEULEU1II222 - 243230 - 251
46639VALVALLEULEU1JJ222 - 243230 - 251
46739VALVALLEULEU1KK222 - 243230 - 251
46839VALVALLEULEU1LL222 - 243230 - 251
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein
Phycocyanobilin:ferredoxin oxidoreductase /


Mass: 28755.631 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: pcyA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q93TN0, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 18% PEG-8000, 25mM MES-NaOH, 50mM Calcium acetate, 10% dioxine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2005 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→43.94 Å / Num. obs: 91664 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.383 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.94 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 22.969 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25716 4583 5 %RANDOM
Rwork0.2109 ---
obs0.21326 86919 99.68 %-
all-91598 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.47 Å2
2---0.86 Å20 Å2
3---1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.354 Å-
Luzzati d res low-2.5 Å
Luzzati sigma a0.265 Å-
Refinement stepCycle: LAST / Resolution: 2.5→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23422 0 1 190 23613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02223998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.96132566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14452906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83524.3161228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.998154062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.01115168
X-RAY DIFFRACTIONr_chiral_restr0.0980.23502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218674
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.29703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.216335
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2851
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2410.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.2299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4761.514997
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.671223648
X-RAY DIFFRACTIONr_scbond_it2.864310023
X-RAY DIFFRACTIONr_scangle_it4.5984.58918
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1473tight positional0.110.05
2B1473tight positional0.130.05
3C1473tight positional0.080.05
4D1473tight positional0.090.05
5E1473tight positional0.080.05
6F1473tight positional0.130.05
7G1473tight positional0.10.05
8H1473tight positional0.120.05
9I1473tight positional0.110.05
10J1473tight positional0.080.05
11K1473tight positional0.160.05
12L1473tight positional0.060.05
1A40medium positional0.540.5
2B40medium positional0.670.5
3C40medium positional0.230.5
4D40medium positional0.250.5
5E40medium positional0.350.5
6F40medium positional0.320.5
7G40medium positional0.330.5
8H40medium positional0.280.5
9I40medium positional0.380.5
10J40medium positional0.760.5
11K40medium positional0.30.5
12L40medium positional0.40.5
1A384loose positional1.155
2B384loose positional0.875
3C384loose positional0.695
4D384loose positional0.725
5E384loose positional0.925
6F384loose positional0.825
7G384loose positional0.75
8H384loose positional0.895
9I384loose positional1.125
10J384loose positional15
11K384loose positional1.055
12L384loose positional0.775
1A1473tight thermal2.5320
2B1473tight thermal2.8620
3C1473tight thermal2.3820
4D1473tight thermal2.5420
5E1473tight thermal2.1120
6F1473tight thermal2.2420
7G1473tight thermal2.2720
8H1473tight thermal2.1720
9I1473tight thermal2.4520
10J1473tight thermal2.5920
11K1473tight thermal3.3320
12L1473tight thermal3.1120
1A40medium thermal1.8340
2B40medium thermal10.6140
3C40medium thermal0.7940
4D40medium thermal3.1740
5E40medium thermal2.2340
6F40medium thermal0.9740
7G40medium thermal2.4140
8H40medium thermal3.6940
9I40medium thermal2.8140
10J40medium thermal10.9840
11K40medium thermal5.8540
12L40medium thermal3.7440
1A384loose thermal3.7380
2B384loose thermal5.3780
3C384loose thermal4.0280
4D384loose thermal4.380
5E384loose thermal4.8280
6F384loose thermal3.580
7G384loose thermal3.780
8H384loose thermal3.7580
9I384loose thermal3.680
10J384loose thermal4.9180
11K384loose thermal7.3780
12L384loose thermal4.3680
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 353 -
Rwork0.248 6392 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6320.8420.26521.02330.82293.47850.105-0.2725-0.2380.393-0.0727-0.00180.50130.0733-0.0323-0.04750.04880.0362-0.21060.0304-0.32266.429-8.67538.967
23.02650.05171.56562.14370.34025.72990.0964-0.1961-0.1424-0.0204-0.002-0.00290.5575-0.3159-0.0944-0.1521-0.0950.0453-0.1026-0.031-0.3301-9.706-8.33684.159
32.797-0.5958-0.14323.48871.06681.86040.05990.0575-0.07460.0252-0.0958-0.2720.11890.06770.0358-0.23590.02010.0248-0.18310.0446-0.3202-20.41-41.46961.678
41.6987-0.02610.0911.0041-0.40163.0545-0.02070.0414-0.0014-0.14070.0420.0420.06140.0485-0.0212-0.28440.00980.014-0.279-0.0157-0.3827-45.75-44.75522.538
52.0836-0.5715-0.94712.60280.76061.720.06260.1941-0.0717-0.1812-0.0893-0.0956-0.07060.02910.0267-0.25770.03830.0246-0.1885-0.0226-0.371-56.905-6.9141.846
62.43620.8747-0.28043.1895-1.19791.81190.1496-0.10030.03790.2885-0.06860.21660.0046-0.0976-0.081-0.2096-0.01850.0321-0.20140.0295-0.39-59.634-42.4359.329
72.34510.2038-0.10212.3556-1.34993.4085-0.0163-0.07030.08740.14780.1102-0.046-0.18340.1005-0.0939-0.20620.06030.0677-0.1863-0.0181-0.3058-6.42325.53123.228
82.2807-0.0433-0.23941.8311-0.68121.54870.0218-0.09560.16390.08030.02180.1449-0.14350.0887-0.0437-0.27420.00180.0555-0.238-0.0158-0.3405-6.971-46.37820.272
92.67280.0558-0.35871.47880.99265.4739-0.1485-0.02970.0451-0.0427-0.01620.11570.29730.02860.1647-0.16730.01930.0389-0.217-0.0509-0.32-46.35825.71524.442
102.6335-0.29350.64812.39321.00742.07540.004-0.08310.05360.06420.0459-0.1559-0.0955-0.0172-0.0499-0.1108-0.00910.0266-0.2555-0.0116-0.3895-33.872-10.59336.356
113.28271.2331-0.91883.2301-0.25181.5734-0.06030.0318-0.19150.1591-0.05120.28440.0118-0.12720.1115-0.2140.01820.0425-0.12110.0375-0.2504-19.056-4.0731.003
124.3988-2.4543-0.55486.0386-0.59892.0763-0.6053-0.2459-0.55420.53730.3540.75760.24190.43470.25130.05050.12620.274-0.11580.1490.1859-48.409-9.97185.851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2459 - 253
2X-RAY DIFFRACTION2BB1 - 2459 - 253
3X-RAY DIFFRACTION3CC1 - 2459 - 253
4X-RAY DIFFRACTION4DD1 - 2459 - 253
5X-RAY DIFFRACTION5EE1 - 2459 - 253
6X-RAY DIFFRACTION6FF1 - 2459 - 253
7X-RAY DIFFRACTION7GG1 - 2459 - 253
8X-RAY DIFFRACTION8HH1 - 2459 - 253
9X-RAY DIFFRACTION9II8 - 24516 - 253
10X-RAY DIFFRACTION10JJ8 - 24516 - 253
11X-RAY DIFFRACTION11KK8 - 24516 - 253
12X-RAY DIFFRACTION12LL8 - 24516 - 253

+
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