[English] 日本語
Yorodumi
- PDB-3cfk: Crystal structure of catalytic elimination antibody 34E4, triclin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cfk
TitleCrystal structure of catalytic elimination antibody 34E4, triclinic crystal form
Components(CATALYTIC ANTIBODY FAB 34E4 ...) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / APO FORM / PROTON TRANSFER / CONFORMATIONAL CHANGE / CHIMERA / Immunoglobulin domain / Immunoglobulin V region
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig-like domain-containing protein / Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDebler, E.W. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Conformational isomerism can limit antibody catalysis.
Authors: Debler, E.W. / Muller, R. / Hilvert, D. / Wilson, I.A.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 19, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description
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_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.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_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
L: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
H: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
A: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
B: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
C: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
D: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
E: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
F: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
G: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
I: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
J: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
K: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
M: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
N: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
O: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
P: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,01943
Polymers383,68516
Non-polymers3,33427
Water4,990277
1
L: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
H: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2985
Polymers47,9612
Non-polymers3373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint21 kcal/mol
Surface area20800 Å2
MethodPISA
2
A: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
B: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3906
Polymers47,9612
Non-polymers4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint16 kcal/mol
Surface area21100 Å2
MethodPISA
3
C: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
D: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5237
Polymers47,9612
Non-polymers5625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint21.4 kcal/mol
Surface area20670 Å2
MethodPISA
4
E: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
F: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2785
Polymers47,9612
Non-polymers3173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint20.4 kcal/mol
Surface area20960 Å2
MethodPISA
5
G: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
I: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4106
Polymers47,9612
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint20.9 kcal/mol
Surface area20890 Å2
MethodPISA
6
J: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
K: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4106
Polymers47,9612
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint21.3 kcal/mol
Surface area20720 Å2
MethodPISA
7
M: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
N: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3554
Polymers47,9612
Non-polymers3952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint16.8 kcal/mol
Surface area21260 Å2
MethodPISA
8
O: CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
P: CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3554
Polymers47,9612
Non-polymers3952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint17.2 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.069, 106.299, 116.109
Angle α, β, γ (deg.)89.89, 90.04, 89.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
31C
41E
51G
61J
71M
81O
12L
22A
32C
42E
52G
62M
72O
13L
23A
33C
43E
53G
63J
73M
83O
14L
24A
34C
44E
54G
64J
74M
84O
15L
25A
35C
45E
55G
65J
75M
85O
16L
26A
36E
46G
17L
27A
37C
47E
57G
67J
77M
87O
18L
28A
38C
48E
58G
68J
78M
88O
19L
29C
39E
49G
59J
69M
79O
110L
210A
310C
410E
510G
610J
710M
810O
111L
211A
311C
411E
511G
611J
711M
811O
112L
212A
312C
412E
512G
612J
712M
812O
113L
213A
313C
413E
513G
613J
713M
813O
114H
214B
314D
414F
514I
614K
714N
814P
115H
215B
315D
415F
515I
615K
715N
815P
116H
216B
316D
416F
516I
616K
716N
816P
117H
217B
317D
417F
517I
617K
717N
817P
118H
218B
318D
418F
518I
618K
718N
818P
119H
219B
319D
419F
519I
619K
719N
819P
120B
220F
320I
420K
520N
620P
121H
221B
321F
421I
521K
621N
721P
122H
222B
322D
422F
522I
622K
722N
822P
123H
223B
323D
423F
523I
623K
723N
823P
124H
224B
324D
424F
524I
624K
724N
824P
125L
225A
325C
425E
525G
625J
725M
825O
126L
226A
326C
426E
526G
626J
726M
826O
127L
227A
327C
427E
527G
627J
727M
827O
128L
228A
328C
428E
528G
628J
728M
828O

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYS1LA3 - 393 - 41
21VALVALLYSLYS1AC3 - 393 - 41
31VALVALLYSLYS1CE3 - 393 - 41
41VALVALLYSLYS1EG3 - 393 - 41
51VALVALLYSLYS1GI3 - 393 - 41
61VALVALLYSLYS1JK3 - 393 - 41
71VALVALLYSLYS1MM3 - 393 - 41
81VALVALLYSLYS1OO3 - 393 - 41
12PROPROPROPRO1LA4042
22PROPROPROPRO1AC4042
32PROPROPROPRO1CE4042
42PROPROPROPRO1EG4042
52PROPROPROPRO1GI4042
62PROPROPROPRO1MM4042
72PROPROPROPRO1OO4042
13ASPASPLEULEU1LA41 - 4343 - 45
23ASPASPLEULEU1AC41 - 4343 - 45
33ASPASPLEULEU1CE41 - 4343 - 45
43ASPASPLEULEU1EG41 - 4343 - 45
53ASPASPLEULEU1GI41 - 4343 - 45
63ASPASPLEULEU1JK41 - 4343 - 45
73ASPASPLEULEU1MM41 - 4343 - 45
83ASPASPLEULEU1OO41 - 4343 - 45
14PHEPHEPHEPHE3LA4446
24PHEPHEPHEPHE3AC4446
34PHEPHEPHEPHE3CE4446
44PHEPHEPHEPHE3EG4446
54PHEPHEPHEPHE3GI4446
64PHEPHEPHEPHE3JK4446
74PHEPHEPHEPHE3MM4446
84PHEPHEPHEPHE3OO4446
15THRTHRLEULEU1LA45 - 6647 - 68
25THRTHRLEULEU1AC45 - 6647 - 68
35THRTHRLEULEU1CE45 - 6647 - 68
45THRTHRLEULEU1EG45 - 6647 - 68
55THRTHRLEULEU1GI45 - 6647 - 68
65THRTHRLEULEU1JK45 - 6647 - 68
75THRTHRLEULEU1MM45 - 6647 - 68
85THRTHRLEULEU1OO45 - 6647 - 68
16ILEILEILEILE1LA6769
26ILEILEILEILE1AC6769
36ILEILEILEILE1EG6769
46ILEILEILEILE1GI6769
17GLYGLYTHRTHR1LA68 - 7670 - 78
27GLYGLYTHRTHR1AC68 - 7670 - 78
37GLYGLYTHRTHR1CE68 - 7670 - 78
47GLYGLYTHRTHR1EG68 - 7670 - 78
57GLYGLYTHRTHR1GI68 - 7670 - 78
67GLYGLYTHRTHR1JK68 - 7670 - 78
77GLYGLYTHRTHR1MM68 - 7670 - 78
87GLYGLYTHRTHR1OO68 - 7670 - 78
18VALVALLYSLYS1LA97 - 10799 - 109
28VALVALLYSLYS1AC97 - 10799 - 109
38VALVALLYSLYS1CE97 - 10799 - 109
48VALVALLYSLYS1EG97 - 10799 - 109
58VALVALLYSLYS1GI97 - 10799 - 109
68VALVALLYSLYS1JK97 - 10799 - 109
78VALVALLYSLYS1MM97 - 10799 - 109
88VALVALLYSLYS1OO97 - 10799 - 109
19ARGARGARGARG1LA108110
29ARGARGARGARG1CE108110
39ARGARGARGARG1EG108110
49ARGARGARGARG1GI108110
59ARGARGARGARG1JK108110
69ARGARGARGARG1MM108110
79ARGARGARGARG1OO108110
110THRTHRASNASN1LA109 - 138111 - 140
210THRTHRASNASN1AC109 - 138111 - 140
310THRTHRASNASN1CE109 - 138111 - 140
410THRTHRASNASN1EG109 - 138111 - 140
510THRTHRASNASN1GI109 - 138111 - 140
610THRTHRASNASN1JK109 - 138111 - 140
710THRTHRASNASN1MM109 - 138111 - 140
810THRTHRASNASN1OO109 - 138111 - 140
111TYRTYRLYSLYS1LA140 - 149142 - 151
211TYRTYRLYSLYS1AC140 - 149142 - 151
311TYRTYRLYSLYS1CE140 - 149142 - 151
411TYRTYRLYSLYS1EG140 - 149142 - 151
511TYRTYRLYSLYS1GI140 - 149142 - 151
611TYRTYRLYSLYS1JK140 - 149142 - 151
711TYRTYRLYSLYS1MM140 - 149142 - 151
811TYRTYRLYSLYS1OO140 - 149142 - 151
112LEULEULEULEU3LA154156
212LEULEULEULEU3AC154156
312LEULEULEULEU3CE154156
412LEULEULEULEU3EG154156
512LEULEULEULEU3GI154156
612LEULEULEULEU3JK154156
712LEULEULEULEU3MM154156
812LEULEULEULEU3OO154156
113GLNGLNGLUGLU1LA155 - 213157 - 215
213GLNGLNGLUGLU1AC155 - 213157 - 215
313GLNGLNGLUGLU1CE155 - 213157 - 215
413GLNGLNGLUGLU1EG155 - 213157 - 215
513GLNGLNGLUGLU1GI155 - 213157 - 215
613GLNGLNGLUGLU1JK155 - 213157 - 215
713GLNGLNGLUGLU1MM155 - 213157 - 215
813GLNGLNGLUGLU1OO155 - 213157 - 215
114LYSLYSARGARG1HB3 - 313 - 31
214LYSLYSARGARG1BD3 - 313 - 31
314LYSLYSARGARG1DF3 - 313 - 31
414LYSLYSARGARG1FH3 - 313 - 31
514LYSLYSARGARG1IJ3 - 313 - 31
614LYSLYSARGARG1KL3 - 313 - 31
714LYSLYSARGARG1NN3 - 313 - 31
814LYSLYSARGARG1PP3 - 313 - 31
115TYRTYRTYRTYR3HB3232
215TYRTYRTYRTYR3BD3232
315TYRTYRTYRTYR3DF3232
415TYRTYRTYRTYR3FH3232
515TYRTYRTYRTYR3IJ3232
615TYRTYRTYRTYR3KL3232
715TYRTYRTYRTYR3NN3232
815TYRTYRTYRTYR3PP3232
116TRPTRPASPASP1HB33 - 5333 - 54
216TRPTRPASPASP1BD33 - 5333 - 54
316TRPTRPASPASP1DF33 - 5333 - 54
416TRPTRPASPASP1FH33 - 5333 - 54
516TRPTRPASPASP1IJ33 - 5333 - 54
616TRPTRPASPASP1KL33 - 5333 - 54
716TRPTRPASPASP1NN33 - 5333 - 54
816TRPTRPASPASP1PP33 - 5333 - 54
117SERSERSERSER3HB5455
217SERSERSERSER3BD5455
317SERSERSERSER3DF5455
417SERSERSERSER3FH5455
517SERSERSERSER3IJ5455
617SERSERSERSER3KL5455
717SERSERSERSER3NN5455
817SERSERSERSER3PP5455
118ARGARGTYRTYR1HB55 - 5956 - 60
218ARGARGTYRTYR1BD55 - 5956 - 60
318ARGARGTYRTYR1DF55 - 5956 - 60
418ARGARGTYRTYR1FH55 - 5956 - 60
518ARGARGTYRTYR1IJ55 - 5956 - 60
618ARGARGTYRTYR1KL55 - 5956 - 60
718ARGARGTYRTYR1NN55 - 5956 - 60
818ARGARGTYRTYR1PP55 - 5956 - 60
119ILEILEARGARG1HB68 - 9469 - 98
219ILEILEARGARG1BD68 - 9469 - 98
319ILEILEARGARG1DF68 - 9469 - 98
419ILEILEARGARG1FH68 - 9469 - 98
519ILEILEARGARG1IJ68 - 9469 - 98
619ILEILEARGARG1KL68 - 9469 - 98
719ILEILEARGARG1NN68 - 9469 - 98
819ILEILEARGARG1PP68 - 9469 - 98
120ASPASPTYRTYR1BD98 - 100102 - 104
220ASPASPTYRTYR1FH98 - 100102 - 104
320ASPASPTYRTYR1IJ98 - 100102 - 104
420ASPASPTYRTYR1KL98 - 100102 - 104
520ASPASPTYRTYR1NN98 - 100102 - 104
620ASPASPTYRTYR1PP98 - 100102 - 104
121TYRTYRSERSER1HB100 - 113104 - 123
221TYRTYRSERSER1BD100 - 113104 - 123
321TYRTYRSERSER1FH100 - 113104 - 123
421TYRTYRSERSER1IJ100 - 113104 - 123
521TYRTYRSERSER1KL100 - 113104 - 123
621TYRTYRSERSER1NN100 - 113104 - 123
721TYRTYRSERSER1PP100 - 113104 - 123
122ALAALATHRTHR1HB114 - 173124 - 175
222ALAALATHRTHR1BD114 - 173124 - 175
322ALAALATHRTHR1DF114 - 173124 - 175
422ALAALATHRTHR1FH114 - 173124 - 175
522ALAALATHRTHR1IJ114 - 173124 - 175
622ALAALATHRTHR1KL114 - 173124 - 175
722ALAALATHRTHR1NN114 - 173124 - 175
822ALAALATHRTHR1PP114 - 173124 - 175
123PHEPHEPHEPHE3HB174176
223PHEPHEPHEPHE3BD174176
323PHEPHEPHEPHE3DF174176
423PHEPHEPHEPHE3FH174176
523PHEPHEPHEPHE3IJ174176
623PHEPHEPHEPHE3KL174176
723PHEPHEPHEPHE3NN174176
823PHEPHEPHEPHE3PP174176
124PROPROVALVAL1HB175 - 223177 - 221
224PROPROVALVAL1BD175 - 223177 - 221
324PROPROVALVAL1DF175 - 223177 - 221
424PROPROVALVAL1FH175 - 223177 - 221
524PROPROVALVAL1IJ175 - 223177 - 221
624PROPROVALVAL1KL175 - 223177 - 221
724PROPROVALVAL1NN175 - 223177 - 221
824PROPROVALVAL1PP175 - 223177 - 221
125GLYGLYGLNGLN3LA77 - 7979 - 81
225GLYGLYGLNGLN3AC77 - 7979 - 81
325GLYGLYGLNGLN3CE77 - 7979 - 81
425GLYGLYGLNGLN3EG77 - 7979 - 81
525GLYGLYGLNGLN3GI77 - 7979 - 81
625GLYGLYGLNGLN3JK77 - 7979 - 81
725GLYGLYGLNGLN3MM77 - 7979 - 81
825GLYGLYGLNGLN3OO77 - 7979 - 81
126THRTHRALAALA1LA80 - 8982 - 91
226THRTHRALAALA1AC80 - 8982 - 91
326THRTHRALAALA1CE80 - 8982 - 91
426THRTHRALAALA1EG80 - 8982 - 91
526THRTHRALAALA1GI80 - 8982 - 91
626THRTHRALAALA1JK80 - 8982 - 91
726THRTHRALAALA1MM80 - 8982 - 91
826THRTHRALAALA1OO80 - 8982 - 91
127VALVALVALVAL3LA150152
227VALVALVALVAL3AC150152
327VALVALVALVAL3CE150152
427VALVALVALVAL3EG150152
527VALVALVALVAL3GI150152
627VALVALVALVAL3JK150152
727VALVALVALVAL3MM150152
827VALVALVALVAL3OO150152
128ASPASPALAALA1LA151 - 153153 - 155
228ASPASPALAALA1AC151 - 153153 - 155
328ASPASPALAALA1CE151 - 153153 - 155
428ASPASPALAALA1EG151 - 153153 - 155
528ASPASPALAALA1GI151 - 153153 - 155
628ASPASPALAALA1JK151 - 153153 - 155
728ASPASPALAALA1MM151 - 153153 - 155
828ASPASPALAALA1OO151 - 153153 - 155

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

-
Components

-
Antibody , 2 types, 16 molecules LACEGJMOHBDFIKNP

#1: Antibody
CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein


Mass: 23258.826 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN OF THE VARIABLE DOMAIN from mouse (RESIDUES 1-107) AND THE CONSTANT DOMAIN from human (UNP RESIDUES 131-239)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Plasmid: P4XH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: Q8TCD0
#2: Antibody
CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein


Mass: 24701.814 Da / Num. of mol.: 8 / Mutation: H108S
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN OF THE VARIABLE DOMAIN from mouse(RESIDUES 1-113) AND THE CONSTANT DOMAIN from human (UNP RESIDUES 133-246)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Plasmid: P4XH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: A8K008, UniProt: Q6N089*PLUS

-
Non-polymers , 4 types, 304 molecules

#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growpH: 6.7
Details: 33% PEG 2000, 0.2M CDCL2, 0.1M BIS- TRIS-PROPANE, PH 6.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 6.70

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2006 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 112380 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 62.1 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.25
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.465 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0L
Resolution: 2.6→41.67 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 25.05 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5643 5 %RANDOM
Rwork0.221 ---
obs0.222 106731 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20.27 Å2-0.14 Å2
2---1.22 Å2-0.2 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26768 0 73 277 27118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02227470
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218374
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.95937392
X-RAY DIFFRACTIONr_angle_other_deg0.9553.00344912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54553496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91524.2221080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.775154424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.36715120
X-RAY DIFFRACTIONr_chiral_restr0.0730.24236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0230596
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025412
X-RAY DIFFRACTIONr_nbd_refined0.2060.24241
X-RAY DIFFRACTIONr_nbd_other0.2020.217362
X-RAY DIFFRACTIONr_nbtor_refined0.1810.212758
X-RAY DIFFRACTIONr_nbtor_other0.0880.215581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2645
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2250.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.261
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4130.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0440.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3171.522307
X-RAY DIFFRACTIONr_mcbond_other0.11.57112
X-RAY DIFFRACTIONr_mcangle_it0.416228216
X-RAY DIFFRACTIONr_scbond_it0.666312018
X-RAY DIFFRACTIONr_scangle_it0.9374.59176
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
11L460tight positional0.030.05
12A460tight positional0.030.05
13C460tight positional0.030.05
14E460tight positional0.030.05
15G460tight positional0.030.05
16J460tight positional0.030.05
17M460tight positional0.030.05
18O460tight positional0.030.05
21L14tight positional0.010.05
22A14tight positional0.010.05
23C14tight positional0.010.05
24E14tight positional0.010.05
25G14tight positional0.020.05
26M14tight positional0.010.05
27O14tight positional0.020.05
31L41tight positional0.020.05
32A41tight positional0.020.05
33C41tight positional0.020.05
34E41tight positional0.020.05
35G41tight positional0.020.05
36J41tight positional0.030.05
37M41tight positional0.020.05
38O41tight positional0.020.05
41L6tight positional0.010.05
42A6tight positional0.020.05
43C6tight positional0.020.05
44E6tight positional0.020.05
45G6tight positional0.010.05
46J6tight positional0.020.05
47M6tight positional0.010.05
48O6tight positional0.010.05
51L265tight positional0.020.05
52A265tight positional0.030.05
53C265tight positional0.020.05
54E265tight positional0.020.05
55G265tight positional0.030.05
56J265tight positional0.020.05
57M265tight positional0.020.05
58O265tight positional0.020.05
61L13tight positional0.010.05
62A13tight positional0.010.05
63E13tight positional0.010.05
64G13tight positional0.010.05
71L103tight positional0.030.05
72A103tight positional0.020.05
73C103tight positional0.030.05
74E103tight positional0.020.05
75G103tight positional0.030.05
76J103tight positional0.030.05
77M103tight positional0.030.05
78O103tight positional0.030.05
81L140tight positional0.020.05
82A140tight positional0.030.05
83C140tight positional0.020.05
84E140tight positional0.020.05
85G140tight positional0.020.05
86J140tight positional0.020.05
87M140tight positional0.020.05
88O140tight positional0.020.05
91L24tight positional0.020.05
92C24tight positional0.020.05
93E24tight positional0.020.05
94G24tight positional0.010.05
95J24tight positional0.010.05
96M24tight positional0.020.05
97O24tight positional0.010.05
101L358tight positional0.030.05
102A358tight positional0.030.05
103C358tight positional0.030.05
104E358tight positional0.030.05
105G358tight positional0.030.05
106J358tight positional0.030.05
107M358tight positional0.130.05
108O358tight positional0.030.05
111L167tight positional0.020.05
112A167tight positional0.020.05
113C167tight positional0.020.05
114E167tight positional0.020.05
115G167tight positional0.020.05
116J167tight positional0.030.05
117M167tight positional0.020.05
118O167tight positional0.030.05
121L6tight positional0.030.05
122A6tight positional0.010.05
123C6tight positional0.020.05
124E6tight positional0.010.05
125G6tight positional0.010.05
126J6tight positional0.010.05
127M6tight positional0.010.05
128O6tight positional0.010.05
131L759tight positional0.030.05
132A759tight positional0.030.05
133C759tight positional0.030.05
134E759tight positional0.020.05
135G759tight positional0.030.05
136J759tight positional0.030.05
137M759tight positional0.030.05
138O759tight positional0.030.05
141H361tight positional0.030.05
142B361tight positional0.020.05
143D361tight positional0.030.05
144F361tight positional0.030.05
145I361tight positional0.020.05
146K361tight positional0.020.05
147N361tight positional0.020.05
148P361tight positional0.020.05
151H6tight positional0.020.05
152B6tight positional0.010.05
153D6tight positional0.020.05
154F6tight positional0.010.05
155I6tight positional0.010.05
156K6tight positional0.020.05
157N6tight positional0.010.05
158P6tight positional0.010.05
161H313tight positional0.030.05
162B313tight positional0.020.05
163D313tight positional0.030.05
164F313tight positional0.020.05
165I313tight positional0.030.05
166K313tight positional0.020.05
167N313tight positional0.020.05
168P313tight positional0.020.05
171H6tight positional0.030.05
172B6tight positional0.030.05
173D6tight positional0.030.05
174F6tight positional0.020.05
175I6tight positional0.020.05
176K6tight positional0.020.05
177N6tight positional0.020.05
178P6tight positional0.020.05
181H79tight positional0.060.05
182B79tight positional0.030.05
183D79tight positional0.050.05
184F79tight positional0.030.05
185I79tight positional0.030.05
186K79tight positional0.030.05
187N79tight positional0.020.05
188P79tight positional0.020.05
191H442tight positional0.030.05
192B442tight positional0.020.05
193D442tight positional0.030.05
194F442tight positional0.020.05
195I442tight positional0.020.05
196K442tight positional0.020.05
197N442tight positional0.020.05
198P442tight positional0.020.05
201B70tight positional0.020.05
202F70tight positional0.010.05
203I70tight positional0.010.05
204K70tight positional0.020.05
205N70tight positional0.020.05
206P70tight positional0.020.05
211H218tight positional0.140.05
212B218tight positional0.040.05
213F218tight positional0.040.05
214I218tight positional0.040.05
215K218tight positional0.030.05
216N218tight positional0.030.05
217P218tight positional0.030.05
221H606tight positional0.030.05
222B606tight positional0.030.05
223D606tight positional0.030.05
224F606tight positional0.030.05
225I606tight positional0.020.05
226K606tight positional0.030.05
227N606tight positional0.030.05
228P606tight positional0.030.05
231H6tight positional0.020.05
232B6tight positional0.020.05
233D6tight positional0.010.05
234F6tight positional0.010.05
235I6tight positional0.020.05
236K6tight positional0.010.05
237N6tight positional0.020.05
238P6tight positional0.020.05
241H549tight positional0.030.05
242B549tight positional0.040.05
243D549tight positional0.030.05
244F549tight positional0.030.05
245I549tight positional0.030.05
246K549tight positional0.030.05
247N549tight positional0.030.05
248P549tight positional0.030.05
251L17tight positional0.020.05
252A17tight positional0.020.05
253C17tight positional0.020.05
254E17tight positional0.020.05
255G17tight positional0.030.05
256J17tight positional0.020.05
257M17tight positional0.020.05
258O17tight positional0.020.05
261L130tight positional0.080.05
262A130tight positional0.030.05
263C130tight positional0.030.05
264E130tight positional0.030.05
265G130tight positional0.030.05
266J130tight positional0.030.05
267M130tight positional0.030.05
268O130tight positional0.030.05
271L6tight positional0.010.05
272A6tight positional0.020.05
273C6tight positional0.020.05
274E6tight positional0.010.05
275G6tight positional0.010.05
276J6tight positional0.010.05
277M6tight positional0.010.05
278O6tight positional0.010.05
281L31tight positional0.060.05
282A31tight positional0.040.05
283C31tight positional0.060.05
284E31tight positional0.030.05
285G31tight positional0.310.05
286J31tight positional0.060.05
287M31tight positional0.060.05
288O31tight positional0.050.05
41L14loose positional0.945
42A14loose positional0.945
43C14loose positional1.565
44E14loose positional0.955
45G14loose positional0.945
46J14loose positional0.955
47M14loose positional1.575
48O14loose positional1.555
121L7loose positional0.865
122A7loose positional0.965
123C7loose positional0.85
124E7loose positional0.865
125G7loose positional0.745
126J7loose positional1.135
127M7loose positional1.725
128O7loose positional1.745
151H14loose positional1.895
152B14loose positional0.655
153D14loose positional1.875
154F14loose positional0.625
155I14loose positional0.655
156K14loose positional0.655
157N14loose positional0.635
158P14loose positional0.635
171H4loose positional0.145
172B4loose positional0.045
173D4loose positional0.125
174F4loose positional0.195
175I4loose positional0.065
176K4loose positional0.135
177N4loose positional0.15
178P4loose positional0.165
231H14loose positional0.965
232B14loose positional0.985
233D14loose positional1.575
234F14loose positional0.945
235I14loose positional1.545
236K14loose positional1.565
237N14loose positional0.945
238P14loose positional0.965
251L12loose positional0.225
252A12loose positional0.195
253C12loose positional0.355
254E12loose positional0.255
255G12loose positional0.275
256J12loose positional0.125
257M12loose positional0.275
258O12loose positional0.395
271L4loose positional0.175
272A4loose positional0.215
273C4loose positional0.125
274E4loose positional0.265
275G4loose positional0.165
276J4loose positional0.135
277M4loose positional0.185
278O4loose positional0.085
11L460tight thermal0.060.5
12A460tight thermal0.070.5
13C460tight thermal0.060.5
14E460tight thermal0.060.5
15G460tight thermal0.060.5
16J460tight thermal0.060.5
17M460tight thermal0.060.5
18O460tight thermal0.070.5
21L14tight thermal0.050.5
22A14tight thermal0.040.5
23C14tight thermal0.060.5
24E14tight thermal0.040.5
25G14tight thermal0.040.5
26M14tight thermal0.050.5
27O14tight thermal0.070.5
31L41tight thermal0.050.5
32A41tight thermal0.060.5
33C41tight thermal0.040.5
34E41tight thermal0.040.5
35G41tight thermal0.070.5
36J41tight thermal0.060.5
37M41tight thermal0.050.5
38O41tight thermal0.060.5
41L6tight thermal0.090.5
42A6tight thermal0.070.5
43C6tight thermal0.070.5
44E6tight thermal0.090.5
45G6tight thermal0.020.5
46J6tight thermal0.080.5
47M6tight thermal0.120.5
48O6tight thermal0.080.5
51L265tight thermal0.050.5
52A265tight thermal0.060.5
53C265tight thermal0.050.5
54E265tight thermal0.070.5
55G265tight thermal0.060.5
56J265tight thermal0.060.5
57M265tight thermal0.060.5
58O265tight thermal0.060.5
61L13tight thermal0.060.5
62A13tight thermal0.060.5
63E13tight thermal0.040.5
64G13tight thermal0.060.5
71L103tight thermal0.060.5
72A103tight thermal0.060.5
73C103tight thermal0.060.5
74E103tight thermal0.060.5
75G103tight thermal0.060.5
76J103tight thermal0.070.5
77M103tight thermal0.060.5
78O103tight thermal0.070.5
81L140tight thermal0.050.5
82A140tight thermal0.060.5
83C140tight thermal0.050.5
84E140tight thermal0.050.5
85G140tight thermal0.060.5
86J140tight thermal0.060.5
87M140tight thermal0.060.5
88O140tight thermal0.060.5
91L24tight thermal0.050.5
92C24tight thermal0.040.5
93E24tight thermal0.070.5
94G24tight thermal0.070.5
95J24tight thermal0.060.5
96M24tight thermal0.040.5
97O24tight thermal0.060.5
101L358tight thermal0.070.5
102A358tight thermal0.060.5
103C358tight thermal0.070.5
104E358tight thermal0.060.5
105G358tight thermal0.070.5
106J358tight thermal0.060.5
107M358tight thermal0.050.5
108O358tight thermal0.060.5
111L167tight thermal0.070.5
112A167tight thermal0.050.5
113C167tight thermal0.070.5
114E167tight thermal0.050.5
115G167tight thermal0.060.5
116J167tight thermal0.060.5
117M167tight thermal0.060.5
118O167tight thermal0.060.5
121L6tight thermal0.030.5
122A6tight thermal0.040.5
123C6tight thermal0.040.5
124E6tight thermal0.040.5
125G6tight thermal0.090.5
126J6tight thermal0.060.5
127M6tight thermal0.050.5
128O6tight thermal0.090.5
131L759tight thermal0.060.5
132A759tight thermal0.060.5
133C759tight thermal0.070.5
134E759tight thermal0.060.5
135G759tight thermal0.070.5
136J759tight thermal0.060.5
137M759tight thermal0.060.5
138O759tight thermal0.050.5
141H361tight thermal0.070.5
142B361tight thermal0.050.5
143D361tight thermal0.060.5
144F361tight thermal0.050.5
145I361tight thermal0.050.5
146K361tight thermal0.050.5
147N361tight thermal0.050.5
148P361tight thermal0.050.5
151H6tight thermal0.050.5
152B6tight thermal0.050.5
153D6tight thermal0.10.5
154F6tight thermal0.020.5
155I6tight thermal0.070.5
156K6tight thermal0.040.5
157N6tight thermal0.060.5
158P6tight thermal0.030.5
161H313tight thermal0.060.5
162B313tight thermal0.060.5
163D313tight thermal0.050.5
164F313tight thermal0.050.5
165I313tight thermal0.050.5
166K313tight thermal0.050.5
167N313tight thermal0.050.5
168P313tight thermal0.050.5
171H6tight thermal0.10.5
172B6tight thermal0.050.5
173D6tight thermal0.090.5
174F6tight thermal0.020.5
175I6tight thermal0.020.5
176K6tight thermal0.070.5
177N6tight thermal0.060.5
178P6tight thermal0.060.5
181H79tight thermal0.070.5
182B79tight thermal0.050.5
183D79tight thermal0.060.5
184F79tight thermal0.050.5
185I79tight thermal0.040.5
186K79tight thermal0.050.5
187N79tight thermal0.040.5
188P79tight thermal0.040.5
191H442tight thermal0.070.5
192B442tight thermal0.060.5
193D442tight thermal0.060.5
194F442tight thermal0.050.5
195I442tight thermal0.050.5
196K442tight thermal0.050.5
197N442tight thermal0.050.5
198P442tight thermal0.050.5
201B70tight thermal0.030.5
202F70tight thermal0.030.5
203I70tight thermal0.030.5
204K70tight thermal0.030.5
205N70tight thermal0.030.5
206P70tight thermal0.020.5
211H218tight thermal0.070.5
212B218tight thermal0.060.5
213F218tight thermal0.050.5
214I218tight thermal0.050.5
215K218tight thermal0.050.5
216N218tight thermal0.050.5
217P218tight thermal0.050.5
221H606tight thermal0.060.5
222B606tight thermal0.060.5
223D606tight thermal0.060.5
224F606tight thermal0.060.5
225I606tight thermal0.060.5
226K606tight thermal0.060.5
227N606tight thermal0.060.5
228P606tight thermal0.060.5
231H6tight thermal0.090.5
232B6tight thermal0.060.5
233D6tight thermal0.070.5
234F6tight thermal0.080.5
235I6tight thermal0.090.5
236K6tight thermal0.050.5
237N6tight thermal0.080.5
238P6tight thermal0.080.5
241H549tight thermal0.070.5
242B549tight thermal0.070.5
243D549tight thermal0.060.5
244F549tight thermal0.060.5
245I549tight thermal0.060.5
246K549tight thermal0.060.5
247N549tight thermal0.060.5
248P549tight thermal0.060.5
251L17tight thermal0.070.5
252A17tight thermal0.070.5
253C17tight thermal0.030.5
254E17tight thermal0.070.5
255G17tight thermal0.040.5
256J17tight thermal0.10.5
257M17tight thermal0.050.5
258O17tight thermal0.070.5
261L130tight thermal0.080.5
262A130tight thermal0.070.5
263C130tight thermal0.070.5
264E130tight thermal0.050.5
265G130tight thermal0.070.5
266J130tight thermal0.070.5
267M130tight thermal0.070.5
268O130tight thermal0.070.5
271L6tight thermal0.10.5
272A6tight thermal0.070.5
273C6tight thermal0.110.5
274E6tight thermal0.110.5
275G6tight thermal0.060.5
276J6tight thermal0.040.5
277M6tight thermal0.040.5
278O6tight thermal0.070.5
281L31tight thermal0.090.5
282A31tight thermal0.050.5
283C31tight thermal0.10.5
284E31tight thermal0.050.5
285G31tight thermal0.160.5
286J31tight thermal0.090.5
287M31tight thermal0.050.5
288O31tight thermal0.060.5
41L14loose thermal0.510
42A14loose thermal0.2910
43C14loose thermal0.5610
44E14loose thermal1.4710
45G14loose thermal0.2410
46J14loose thermal1.2210
47M14loose thermal0.3810
48O14loose thermal0.410
121L7loose thermal0.3810
122A7loose thermal0.5210
123C7loose thermal0.2810
124E7loose thermal0.4110
125G7loose thermal0.4710
126J7loose thermal0.3510
127M7loose thermal1.0310
128O7loose thermal0.8410
151H14loose thermal0.2410
152B14loose thermal0.6110
153D14loose thermal0.2510
154F14loose thermal0.2610
155I14loose thermal0.4410
156K14loose thermal0.5310
157N14loose thermal0.8810
158P14loose thermal0.1210
171H4loose thermal0.610
172B4loose thermal1.1510
173D4loose thermal0.5910
174F4loose thermal0.2210
175I4loose thermal0.4710
176K4loose thermal0.2910
177N4loose thermal0.2210
178P4loose thermal0.3510
231H14loose thermal0.7710
232B14loose thermal0.4610
233D14loose thermal0.4710
234F14loose thermal0.6810
235I14loose thermal0.7310
236K14loose thermal0.4410
237N14loose thermal0.5610
238P14loose thermal1.2910
251L12loose thermal0.5910
252A12loose thermal0.9310
253C12loose thermal0.5310
254E12loose thermal0.6710
255G12loose thermal2.4510
256J12loose thermal0.7110
257M12loose thermal0.6310
258O12loose thermal1.8810
271L4loose thermal0.2110
272A4loose thermal0.6910
273C4loose thermal0.810
274E4loose thermal0.5710
275G4loose thermal0.5610
276J4loose thermal0.3210
277M4loose thermal0.2110
278O4loose thermal0.5910
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 374 -
Rwork0.346 7007 -
obs--83.44 %
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)
14.35480.1794-1.11476.9813-0.26285.0972-0.0256-0.1707-0.32510.11790.1095-0.2332-0.03740.0128-0.0839-0.1435-0.02290.0539-0.33130.0055-0.1719-2.0318-3.206335.2824
24.57053.7313-1.0788.52380.15393.9752-0.0681-0.18720.07090.1104-0.194-0.20430.28050.24210.2621-0.41160.06680.052-0.16040.0266-0.255919.76122.080422.4512
35.72891.52770.0776.16110.20575.34810.1822-0.3401-0.23820.3863-0.13590.0979-0.00030.2327-0.0463-0.139-0.04130.1287-0.25290.033-0.3055-13.732712.424443.7497
42.9046-0.1088-1.62293.90631.761210.26140.12580.38680.4624-0.0868-0.06060.1877-0.2038-0.1146-0.0652-0.4038-0.00270.0698-0.20270.0241-0.14355.281527.875921.9649
57.12291.1341-0.11468.27230.26023.5066-0.03970.16290.18870.420.1260.5296-0.12080.1773-0.0863-0.1851-0.01190.0547-0.3217-0.0166-0.24267.329981.954429.4445
66.79261.5769-2.076412.6474-3.72753.25730.0507-0.64080.151.2578-0.06970.79280.16240.1590.0190.0330.01510.2484-0.1617-0.0414-0.2475-12.598756.231544.9048
74.75250.0259-0.42787.4478-2.24396.85480.11010.0474-0.09960.1001-0.0788-0.5301-0.34120.7348-0.0313-0.3043-0.0385-0.0043-0.1472-0.0875-0.182719.57966.351521.3807
89.7418-2.74760.60365.0687-0.53193.34420.07980.4172-0.25870.2562-0.14860.56920.2368-0.25760.0688-0.14190.00430.1144-0.2453-0.0164-0.2495-7.702350.92431.007
95.1009-0.31441.58516.9529-0.06284.16150.0186-0.18520.26950.20430.0980.20020.02550.0185-0.1167-0.1429-0.0184-0.0189-0.3395-0.0195-0.178932.030952.8021-22.9263
104.3032.9910.88968.2038-0.64023.702-0.0126-0.1243-0.1320.1672-0.18590.1106-0.2728-0.26850.1985-0.42220.0548-0.0503-0.1555-0.0341-0.241310.158427.4182-35.6235
115.72371.45670.09236.9212-0.04734.56090.1209-0.44990.2040.4817-0.088-0.1710.002-0.2862-0.0329-0.1511-0.0472-0.1447-0.21-0.0129-0.278443.683837.223-14.2547
123.2239-0.33451.72473.954-1.965110.17420.15310.3517-0.3606-0.0523-0.0857-0.16120.23860.161-0.0675-0.4068-0.0058-0.0609-0.2538-0.0419-0.062824.630821.5944-36.0034
135.8481.4260.18449.1754-0.463.1623-0.03840.031-0.01750.59490.1131-0.42130.0893-0.1944-0.0747-0.1683-0.0046-0.0093-0.30950.0089-0.23222.7055-32.3904-28.7646
147.30031.66942.272913.38494.47632.97320.3072-0.8533-0.35451.4164-0.197-0.9605-0.0995-0.1651-0.11020.1637-0.0411-0.2664-0.10340.087-0.143842.7277-6.8115-13.3095
155.49790.4230.07747.14422.36176.56320.12450.02530.16910.1586-0.00860.5690.2431-0.7993-0.1159-0.26530.00880.0553-0.12810.1166-0.131510.3872-16.7666-36.6865
1611.213-3.055-1.16245.1536-0.30133.06660.09820.26440.32420.4457-0.1283-0.4858-0.35280.24810.0301-0.0553-0.0009-0.0897-0.2598-0.0326-0.216637.7429-1.4004-27.1655
174.32910.68441.3865.59620.64944.87470.17780.34960.0556-0.19670.24710.1176-0.0483-0.0825-0.4249-0.06770.08310.1594-0.23940.0874-0.256942.217452.3593-56.0047
184.5353-4.44730.43028.96560.23093.32490.16440.1712-0.3165-0.2635-0.1967-0.0868-0.19320.18170.0323-0.4042-0.0348-0.0464-0.2287-0.0187-0.194864.086927.2434-42.6895
197.8776-1.249-0.97786.95270.86594.72430.12060.96810.2526-0.56840.0394-0.0434-0.0675-0.3924-0.16-0.0331-0.0017-0.08980.03790.1311-0.305730.612636.6347-64.7392
202.93450.38931.72355.26051.899710.28040.1555-0.308-0.4698-0.0454-0.0870.24840.2549-0.4334-0.0686-0.38790.0098-0.0537-0.2208-0.0464-0.011249.599721.414-42.5499
214.04430.3976-1.37376.69240.19646.31690.08530.3406-0.1453-0.17730.2469-0.03550.06980.1669-0.3322-0.06090.0664-0.0866-0.255-0.1044-0.2853-12.359-3.00492.0597
224.5344-4.0429-0.85147.621-0.10624.05980.11680.17250.2692-0.1624-0.1466-0.08260.1288-0.18370.0298-0.3998-0.03930.0291-0.2290.0157-0.189-34.189222.209415.2898
236.9003-1.69030.37236.3286-0.58214.25060.13210.9959-0.3286-0.56490.0390.10540.11950.4335-0.17110.0272-0.06890.06150.0552-0.1461-0.26-0.772612.5707-6.5883
241.6710.3795-1.73745.8744-1.56459.27670.1173-0.23380.4333-0.0075-0.0417-0.1439-0.26160.4066-0.0756-0.40680.00310.0498-0.15760.0117-0.0498-19.699328.016115.4141
256.0047-2.119-1.83288.46990.33073.3324-0.0148-0.0177-0.1643-0.4459-0.00480.3005-0.1526-0.20680.0196-0.07770.0799-0.2559-0.3131-0.1112-0.1382-19.643982.19327.804
265.5730.44660.33018.95272.99523.7424-0.0650.5128-0.2266-0.7291-0.1617-0.03880.2436-0.040.22670.09080.0230.0425-0.1519-0.0374-0.35090.405657.239-8.4663
273.95890.6177-0.49725.66323.09077.9968-0.1214-0.0426-0.2285-0.4661-0.18620.8721-0.5666-0.83640.3076-0.24810.1015-0.1523-0.0784-0.08190.3312-32.148166.605215.382
2811.05021.90230.74344.63680.07881.7693-0.0644-0.52-0.6221-0.2885-0.14990.00880.28830.26110.2144-0.0621-0.01250.0382-0.1782-0.0179-0.2781-4.872651.15985.0276
295.3675-1.4451.07648.6071-0.31893.2925-0.15860.03160.2534-0.17540.0639-0.39250.21580.26990.0948-0.08450.08530.2493-0.31310.1-0.183649.5125-32.824-50.3738
305.42230.7703-0.22038.3973-2.10923.4643-0.13750.49980.2012-0.7242-0.0160.1763-0.32320.02850.15350.0356-0.0063-0.0052-0.14690.039-0.338229.5301-7.7938-66.6038
312.47490.40170.25096.7531-3.92019.2724-0.0716-0.09610.068-0.3706-0.253-0.77660.54020.89670.3246-0.25130.07960.0535-0.02650.10990.241262.1185-17.2579-42.9265
3210.02572.0687-1.42424.5309-0.76861.5534-0.0402-0.54840.4813-0.1896-0.11240.1257-0.2678-0.18390.1526-0.0777-0.01740.0045-0.16550.0125-0.269434.8875-1.6972-53.1454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1071 - 109
2X-RAY DIFFRACTION2LA108 - 213110 - 215
3X-RAY DIFFRACTION3HB1 - 1131 - 123
4X-RAY DIFFRACTION4HB114 - 228124 - 224
5X-RAY DIFFRACTION5AC1 - 1071 - 109
6X-RAY DIFFRACTION6AC108 - 213110 - 215
7X-RAY DIFFRACTION7BD1 - 1131 - 123
8X-RAY DIFFRACTION8BD114 - 228124 - 224
9X-RAY DIFFRACTION9CE1 - 1071 - 109
10X-RAY DIFFRACTION10CE108 - 213110 - 215
11X-RAY DIFFRACTION11DF1 - 1131 - 123
12X-RAY DIFFRACTION12DF114 - 228124 - 224
13X-RAY DIFFRACTION13EG1 - 1071 - 109
14X-RAY DIFFRACTION14EG108 - 213110 - 215
15X-RAY DIFFRACTION15FH1 - 1131 - 123
16X-RAY DIFFRACTION16FH114 - 228124 - 224
17X-RAY DIFFRACTION17GI1 - 1071 - 109
18X-RAY DIFFRACTION18GI108 - 213110 - 215
19X-RAY DIFFRACTION19IJ1 - 1131 - 123
20X-RAY DIFFRACTION20IJ114 - 228124 - 224
21X-RAY DIFFRACTION21JK1 - 1071 - 109
22X-RAY DIFFRACTION22JK108 - 213110 - 215
23X-RAY DIFFRACTION23KL1 - 1131 - 123
24X-RAY DIFFRACTION24KL114 - 228124 - 224
25X-RAY DIFFRACTION25MM1 - 1071 - 109
26X-RAY DIFFRACTION26MM108 - 213110 - 215
27X-RAY DIFFRACTION27NN1 - 1131 - 123
28X-RAY DIFFRACTION28NN114 - 228124 - 224
29X-RAY DIFFRACTION29OO1 - 1071 - 109
30X-RAY DIFFRACTION30OO108 - 213110 - 215
31X-RAY DIFFRACTION31PP1 - 1131 - 123
32X-RAY DIFFRACTION32PP114 - 228124 - 224

+
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