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- PDB-2bb6: Structure of Cobalamin-complexed Bovine Transcobalamin in Monocli... -

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Basic information

Entry
Database: PDB / ID: 2bb6
TitleStructure of Cobalamin-complexed Bovine Transcobalamin in Monoclinic Crystal Form
ComponentsTranscobalamin IITranscobalamin
KeywordsTRANSPORT PROTEIN / alpha_6 - alpha_6 barrel
Function / homology
Function and homology information


Transport of RCbl within the body / cobalt ion transport / cobalamin transport / cobalamin binding / extracellular space / metal ion binding
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALAMIN / Transcobalamin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for mammalian vitamin B12 transport by transcobalamin.
Authors: Wuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Transcobalamin II
B: Transcobalamin II
C: Transcobalamin II
D: Transcobalamin II
A: COBALAMIN
B: COBALAMIN
C: COBALAMIN
D: COBALAMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,72412
Polymers185,2614
Non-polymers5,4638
Water13,763764
1
A: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6813
Polymers46,3151
Non-polymers1,3662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6813
Polymers46,3151
Non-polymers1,3662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6813
Polymers46,3151
Non-polymers1,3662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6813
Polymers46,3151
Non-polymers1,3662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.826, 100.664, 99.143
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B
451A
461B
471A
481B
491A
501B
511A
521B
531A
541B
551A
561B
571A
581B
591A
601B
12C
22D
32C
42D
52C
62D
72C
82D
92C
102D
112C
122D
132C
142D
152C
162D
172C
182D
192C
202D
212C
222D
232C
242D
252C
262D
272C
282D
292C
302D
312C
322D
332C
342D
352C
362D
372C
382D
392C
402D
412C
422D
432C
442D
452C
462D
472C
482D
492C
502D
512C
522D
532C
542D
552C
562D
572C
582D
592C
602D
13A
23C
33A
43C
53A
63C
73A
83C
93A
103C
113A
123C
133A
143C
153A
163C
173A
183C
193A
203C
213A
223C
233A
243C
253A
263C
273A
283C
293A
303C
313A
323C
333A
343C
353A
363C
373A
383C
393A
403C
413A
423C
433A
443C
453A
463C
473A
483C
493A
503C
513A
523C
533A
543C
553A
563C
573A
583C
593A
603C
613A
623C
633A
643C
653A
663C
673A
683C
693A
703C
713A
723C
14A
24D
34A
44D
54A
64D
74A
84D
94A
104D
114A
124D
134A
144D
154A
164D
174A
184D
194A
204D
214A
224D
234A
244D
254A
264D
274A
284D
294A
304D
314A
324D
334A
344D
354A
364D
374A
384D
394A
404D
414A
424D
434A
444D
454A
464D
474A
484D
494A
504D
514A
524D
534A
544D
554A
564D
574A
584D
594A
604D
614A
624D
634A
644D
654A
664D
674A
684D
694A
704D
714A
724D
734A
744D
754A
764D
15B
25C
35B
45C
55B
65C
75B
85C
95B
105C
115B
125C
135B
145C
155B
165C
175B
185C
195B
205C
215B
225C
235B
245C
255B
265C
275B
285C
295B
305C
315B
325C
335B
345C
355B
365C
375B
385C
395B
405C
415B
425C
435B
445C
455B
465C
475B
485C
495B
505C
515B
525C
535B
545C
555B
565C
575B
585C
595B
605C
615B
625C
635B
645C
655B
665C
675B
685C
695B
705C
715B
725C
16B
26D
36B
46D
56B
66D
76B
86D
96B
106D
116B
126D
136B
146D
156B
166D
176B
186D
196B
206D
216B
226D
236B
246D
256B
266D
276B
286D
296B
306D
316B
326D
336B
346D
356B
366D
376B
386D
396B
406D
416B
426D
436B
446D
456B
466D
476B
486D
496B
506D
516B
526D
536B
546D
556B
566D
576B
586D
596B
606D
616B
626D
636B
646D
656B
666D
676B
686D
696B
706D
716B
726D
736B
746D
756B
766D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNTHR1AA1 - 61 - 6
211ASNTHR1BB1 - 61 - 6
321GLUGLU2AA77
421GLUGLU2BB77
531VALGLN1AA8 - 638 - 63
631VALGLN1BB8 - 638 - 63
741ARGALA6AA68 - 8068 - 80
841ARGALA6BB68 - 8068 - 80
951LYSLYS1AA81 - 11481 - 114
1051LYSLYS1BB81 - 11481 - 114
1161ARGARG2AA115115
1261ARGARG2BB115115
1371PHELYS1AA116 - 121116 - 121
1471PHELYS1BB116 - 121116 - 121
1581HISGLN4AA126 - 129126 - 129
1681HISGLN4BB126 - 129126 - 129
1791GLYGLU1AA130 - 166130 - 166
1891GLYGLU1BB130 - 166130 - 166
19101HISASP5AA167 - 174167 - 174
20101HISASP5BB167 - 174167 - 174
21111HISGLN1AA175 - 200175 - 200
22111HISGLN1BB175 - 200175 - 200
23121ARGARG2AA201201
24121ARGARG2BB201201
25131ASNMET1AA202 - 239202 - 239
26131ASNMET1BB202 - 239202 - 239
27141GLYPRO4AA240 - 244240 - 244
28141GLYPRO4BB240 - 244240 - 244
29151SERVAL1AA245 - 246245 - 246
30151SERVAL1BB245 - 246245 - 246
31161GLUGLU2AA247247
32161GLUGLU2BB247247
33171LEUGLN1AA248 - 264248 - 264
34171LEUGLN1BB248 - 264248 - 264
35181HISLYS2AA265 - 266265 - 266
36181HISLYS2BB265 - 266265 - 266
37191THRPRO1AA267 - 303267 - 303
38191THRPRO1BB267 - 303267 - 303
39201ALAGLN6AA304 - 310304 - 310
40201ALAGLN6BB304 - 310304 - 310
41211ALAVAL4AA311 - 313311 - 313
42211ALAVAL4BB311 - 313311 - 313
43221PROPHE1AA314 - 355314 - 355
44221PROPHE1BB314 - 355314 - 355
45231LYSLYS2AA375375
46231LYSLYS2BB375375
47241ALATRP1AA376 - 414376 - 414
48241ALATRP1BB376 - 414376 - 414
49251GLNGLN2AA6464
50251GLNGLN2BB6464
51261SERLEU1AA65 - 6765 - 67
52261SERLEU1BB65 - 6765 - 67
53271ARGARG3AA122122
54271ARGARG3BB122122
55281ALAGLY1AA123 - 125123 - 125
56281ALAGLY1BB123 - 125123 - 125
57291ARGARG2AA356 - 358356 - 358
58291ARGARG2BB356 - 358356 - 358
59301THRARG1AA359 - 374359 - 374
60301THRARG1BB359 - 374359 - 374
112ASNTHR1CC1 - 61 - 6
212ASNTHR1DD1 - 61 - 6
322GLUGLU2CC77
422GLUGLU2DD77
532VALTHR1CC8 - 118 - 11
632VALTHR1DD8 - 118 - 11
742ARGALA6CC68 - 8068 - 80
842ARGALA6DD68 - 8068 - 80
952LYSLYS1CC81 - 11481 - 114
1052LYSLYS1DD81 - 11481 - 114
1162ARGARG2CC115115
1262ARGARG2DD115115
1372PHELYS1CC116 - 121116 - 121
1472PHELYS1DD116 - 121116 - 121
1582HISGLN4CC126 - 129126 - 129
1682HISGLN4DD126 - 129126 - 129
1792GLYGLU1CC130 - 166130 - 166
1892GLYGLU1DD130 - 166130 - 166
19102HISHIS4CC167167
20102HISHIS4DD167167
21112LYSPRO6CC168 - 169168 - 169
22112LYSPRO6DD168 - 169168 - 169
23122HISASP4CC170 - 174170 - 174
24122HISASP4DD170 - 174170 - 174
25132HISGLN1CC175 - 200175 - 200
26132HISGLN1DD175 - 200175 - 200
27142ARGARG2CC201201
28142ARGARG2DD201201
29152ASNMET1CC202 - 239202 - 239
30152ASNMET1DD202 - 239202 - 239
31162GLYPRO2CC240 - 244240 - 244
32162GLYPRO2DD240 - 244240 - 244
33172SERVAL1CC245 - 246245 - 246
34172SERVAL1DD245 - 246245 - 246
35182GLUGLU2CC247247
36182GLUGLU2DD247247
37192LEUHIS1CC248 - 265248 - 265
38192LEUHIS1DD248 - 265248 - 265
39202LYSLYS2CC266266
40202LYSLYS2DD266266
41212THRPRO1CC267 - 303267 - 303
42212THRPRO1DD267 - 303267 - 303
43222VALVAL6CC313313
44222VALVAL6DD313313
45232PROPRO4CC314314
46232PROPRO4DD314314
47242LYSARG1CC315 - 374315 - 374
48242LYSARG1DD315 - 374315 - 374
49252LYSLYS2CC375375
50252LYSLYS2DD375375
51262ALATRP1CC376 - 414376 - 414
52262ALATRP1DD376 - 414376 - 414
53272LEULEU3CC1212
54272LEULEU3DD1212
55282VALLEU1CC13 - 6713 - 67
56282VALLEU1DD13 - 6713 - 67
57292ARGARG2CC122122
58292ARGARG2DD122122
59302ALAGLY1CC123 - 125123 - 125
60302ALAGLY1DD123 - 125123 - 125
113ASNILE1AA1 - 51 - 5
213ASNILE1CC1 - 51 - 5
323THRGLU2AA6 - 76 - 7
423THRGLU2CC6 - 76 - 7
533VALSER1AA8 - 288 - 28
633VALSER1CC8 - 288 - 28
743GLNGLN2AA29 - 3129 - 31
843GLNGLN2CC29 - 3129 - 31
953LEUGLY1AA32 - 3932 - 39
1053LEUGLY1CC32 - 3932 - 39
1163LEULEU2AA4040
1263LEULEU2CC4040
1373ARGLYS1AA41 - 5941 - 59
1473ARGLYS1CC41 - 5941 - 59
1583LEULEU2AA60 - 6760 - 67
1683LEULEU2CC60 - 6760 - 67
1793ARGALA6AA68 - 8068 - 80
1893ARGALA6CC68 - 8068 - 80
19103LYSGLY1AA81 - 10381 - 103
20103LYSGLY1CC81 - 10381 - 103
21113ARGLYS2AA104 - 105104 - 105
22113ARGLYS2CC104 - 105104 - 105
23123GLYLYS1AA106 - 114106 - 114
24123GLYLYS1CC106 - 114106 - 114
25133ARGARG2AA115115
26133ARGARG2CC115115
27143PHELYS1AA116 - 121116 - 121
28143PHELYS1CC116 - 121116 - 121
29153ARGARG3AA122122
30153ARGARG3CC122122
31163ALAGLY1AA123 - 125123 - 125
32163ALAGLY1CC123 - 125123 - 125
33173HISGLN6AA126 - 129126 - 129
34173HISGLN6CC126 - 129126 - 129
35183GLYGLU1AA130 - 166130 - 166
36183GLYGLU1CC130 - 166130 - 166
37193HISHIS6AA167 - 170167 - 170
38193HISHIS6CC167 - 170167 - 170
39203LEUASP5AA171 - 174171 - 174
40203LEUASP5CC171 - 174171 - 174
41213HISGLN1AA175 - 200175 - 200
42213HISGLN1CC175 - 200175 - 200
43223ARGARG2AA201201
44223ARGARG2CC201201
45233ASNMET1AA202 - 239202 - 239
46233ASNMET1CC202 - 239202 - 239
47243GLYPRO6AA240 - 244240 - 244
48243GLYPRO6CC240 - 244240 - 244
49253SERVAL1AA245 - 246245 - 246
50253SERVAL1CC245 - 246245 - 246
51263GLUGLU2AA247247
52263GLUGLU2CC247247
53273LEUHIS1AA248 - 265248 - 265
54273LEUHIS1CC248 - 265248 - 265
55283LYSLYS2AA266266
56283LYSLYS2CC266266
57293THRPRO1AA267 - 303267 - 303
58293THRPRO1CC267 - 303267 - 303
59303PROPRO4AA314314
60303PROPRO4CC314314
61313LYSLYS1AA315 - 347315 - 347
62313LYSLYS1CC315 - 347315 - 347
63323ASNARG2AA348 - 358348 - 358
64323ASNARG2CC348 - 358348 - 358
65333THRARG1AA359 - 374359 - 374
66333THRARG1CC359 - 374359 - 374
67343LYSLYS2AA375375
68343LYSLYS2CC375375
69353ALAVAL1AA376 - 412376 - 412
70353ALAVAL1CC376 - 412376 - 412
71363GLYTRP4AA413 - 414413 - 414
72363GLYTRP4CC413 - 414413 - 414
114ASNILE1AA1 - 51 - 5
214ASNILE1DD1 - 51 - 5
324THRGLU2AA6 - 76 - 7
424THRGLU2DD6 - 76 - 7
534VALTHR1AA8 - 118 - 11
634VALTHR1DD8 - 118 - 11
744GLNGLN2AA29 - 3129 - 31
844GLNGLN2DD29 - 3129 - 31
954LEUGLY1AA32 - 3932 - 39
1054LEUGLY1DD32 - 3932 - 39
1164LEULEU2AA4040
1264LEULEU2DD4040
1374ARGLYS1AA41 - 5941 - 59
1474ARGLYS1DD41 - 5941 - 59
1584LEULEU2AA60 - 6760 - 67
1684LEULEU2DD60 - 6760 - 67
1794ARGALA6AA68 - 8068 - 80
1894ARGALA6DD68 - 8068 - 80
19104LYSGLY1AA81 - 10381 - 103
20104LYSGLY1DD81 - 10381 - 103
21114ARGLYS2AA104 - 105104 - 105
22114ARGLYS2DD104 - 105104 - 105
23124GLYLYS1AA106 - 114106 - 114
24124GLYLYS1DD106 - 114106 - 114
25134ARGARG2AA115115
26134ARGARG2DD115115
27144PHELYS1AA116 - 121116 - 121
28144PHELYS1DD116 - 121116 - 121
29154ARGARG3AA122122
30154ARGARG3DD122122
31164ALAGLY1AA123 - 125123 - 125
32164ALAGLY1DD123 - 125123 - 125
33174HISGLN6AA126 - 129126 - 129
34174HISGLN6DD126 - 129126 - 129
35184GLYGLU1AA130 - 166130 - 166
36184GLYGLU1DD130 - 166130 - 166
37194HISHIS6AA167 - 170167 - 170
38194HISHIS6DD167 - 170167 - 170
39204LEUASP5AA171 - 174171 - 174
40204LEUASP5DD171 - 174171 - 174
41214HISGLN1AA175 - 200175 - 200
42214HISGLN1DD175 - 200175 - 200
43224ARGARG2AA201201
44224ARGARG2DD201201
45234ASNMET1AA202 - 239202 - 239
46234ASNMET1DD202 - 239202 - 239
47244GLYPRO6AA240 - 244240 - 244
48244GLYPRO6DD240 - 244240 - 244
49254SERVAL1AA245 - 246245 - 246
50254SERVAL1DD245 - 246245 - 246
51264GLUGLU2AA247247
52264GLUGLU2DD247247
53274LEUHIS1AA248 - 265248 - 265
54274LEUHIS1DD248 - 265248 - 265
55284LYSLYS2AA266266
56284LYSLYS2DD266266
57294THRPRO1AA267 - 303267 - 303
58294THRPRO1DD267 - 303267 - 303
59304PROPRO4AA314314
60304PROPRO4DD314314
61314LYSLYS1AA315 - 347315 - 347
62314LYSLYS1DD315 - 347315 - 347
63324ASNARG2AA348 - 358348 - 358
64324ASNARG2DD348 - 358348 - 358
65334THRARG1AA359 - 374359 - 374
66334THRARG1DD359 - 374359 - 374
67344LYSLYS2AA375375
68344LYSLYS2DD375375
69354ALAVAL1AA376 - 412376 - 412
70354ALAVAL1DD376 - 412376 - 412
71364LEULEU3AA1212
72364LEULEU3DD1212
73374VALSER1AA13 - 2813 - 28
74374VALSER1DD13 - 2813 - 28
75384GLYTRP4AA413 - 414413 - 414
76384GLYTRP4DD413 - 414413 - 414
115ASNILE1BB1 - 51 - 5
215ASNILE1CC1 - 51 - 5
325THRGLU2BB6 - 76 - 7
425THRGLU2CC6 - 76 - 7
535VALSER1BB8 - 288 - 28
635VALSER1CC8 - 288 - 28
745GLNGLN2BB29 - 3129 - 31
845GLNGLN2CC29 - 3129 - 31
955LEUGLY1BB32 - 3932 - 39
1055LEUGLY1CC32 - 3932 - 39
1165LEULEU2BB4040
1265LEULEU2CC4040
1375ARGLYS1BB41 - 5941 - 59
1475ARGLYS1CC41 - 5941 - 59
1585LEULEU2BB60 - 6760 - 67
1685LEULEU2CC60 - 6760 - 67
1795ARGALA6BB68 - 8068 - 80
1895ARGALA6CC68 - 8068 - 80
19105LYSGLY1BB81 - 10381 - 103
20105LYSGLY1CC81 - 10381 - 103
21115ARGLYS2BB104 - 105104 - 105
22115ARGLYS2CC104 - 105104 - 105
23125GLYLYS1BB106 - 114106 - 114
24125GLYLYS1CC106 - 114106 - 114
25135ARGARG2BB115115
26135ARGARG2CC115115
27145PHELYS1BB116 - 121116 - 121
28145PHELYS1CC116 - 121116 - 121
29155ARGARG3BB122122
30155ARGARG3CC122122
31165ALAGLY1BB123 - 125123 - 125
32165ALAGLY1CC123 - 125123 - 125
33175HISGLN6BB126 - 129126 - 129
34175HISGLN6CC126 - 129126 - 129
35185GLYGLU1BB130 - 166130 - 166
36185GLYGLU1CC130 - 166130 - 166
37195HISHIS6BB167 - 170167 - 170
38195HISHIS6CC167 - 170167 - 170
39205LEUASP5BB171 - 174171 - 174
40205LEUASP5CC171 - 174171 - 174
41215HISGLN1BB175 - 200175 - 200
42215HISGLN1CC175 - 200175 - 200
43225ARGARG2BB201201
44225ARGARG2CC201201
45235ASNMET1BB202 - 239202 - 239
46235ASNMET1CC202 - 239202 - 239
47245GLYPRO6BB240 - 244240 - 244
48245GLYPRO6CC240 - 244240 - 244
49255SERVAL1BB245 - 246245 - 246
50255SERVAL1CC245 - 246245 - 246
51265GLUGLU2BB247247
52265GLUGLU2CC247247
53275LEUHIS1BB248 - 265248 - 265
54275LEUHIS1CC248 - 265248 - 265
55285LYSLYS2BB266266
56285LYSLYS2CC266266
57295THRPRO1BB267 - 303267 - 303
58295THRPRO1CC267 - 303267 - 303
59305PROPRO4BB314314
60305PROPRO4CC314314
61315LYSLYS1BB315 - 347315 - 347
62315LYSLYS1CC315 - 347315 - 347
63325ASNARG2BB348 - 358348 - 358
64325ASNARG2CC348 - 358348 - 358
65335THRARG1BB359 - 374359 - 374
66335THRARG1CC359 - 374359 - 374
67345LYSLYS2BB375375
68345LYSLYS2CC375375
69355ALAVAL1BB376 - 412376 - 412
70355ALAVAL1CC376 - 412376 - 412
71365GLYTRP4BB413 - 414413 - 414
72365GLYTRP4CC413 - 414413 - 414
116ASNILE1BB1 - 51 - 5
216ASNILE1DD1 - 51 - 5
326THRGLU2BB6 - 76 - 7
426THRGLU2DD6 - 76 - 7
536VALTHR1BB8 - 118 - 11
636VALTHR1DD8 - 118 - 11
746GLNGLN2BB29 - 3129 - 31
846GLNGLN2DD29 - 3129 - 31
956LEUGLY1BB32 - 3932 - 39
1056LEUGLY1DD32 - 3932 - 39
1166LEULEU2BB4040
1266LEULEU2DD4040
1376ARGLYS1BB41 - 5941 - 59
1476ARGLYS1DD41 - 5941 - 59
1586LEULEU2BB60 - 6760 - 67
1686LEULEU2DD60 - 6760 - 67
1796ARGALA6BB68 - 8068 - 80
1896ARGALA6DD68 - 8068 - 80
19106LYSGLY1BB81 - 10381 - 103
20106LYSGLY1DD81 - 10381 - 103
21116ARGLYS2BB104 - 105104 - 105
22116ARGLYS2DD104 - 105104 - 105
23126GLYLYS1BB106 - 114106 - 114
24126GLYLYS1DD106 - 114106 - 114
25136ARGARG2BB115115
26136ARGARG2DD115115
27146PHELYS1BB116 - 121116 - 121
28146PHELYS1DD116 - 121116 - 121
29156ARGARG3BB122122
30156ARGARG3DD122122
31166ALAGLY1BB123 - 125123 - 125
32166ALAGLY1DD123 - 125123 - 125
33176HISGLN6BB126 - 129126 - 129
34176HISGLN6DD126 - 129126 - 129
35186GLYGLU1BB130 - 166130 - 166
36186GLYGLU1DD130 - 166130 - 166
37196HISHIS6BB167 - 170167 - 170
38196HISHIS6DD167 - 170167 - 170
39206LEUASP5BB171 - 174171 - 174
40206LEUASP5DD171 - 174171 - 174
41216HISGLN1BB175 - 200175 - 200
42216HISGLN1DD175 - 200175 - 200
43226ARGARG2BB201201
44226ARGARG2DD201201
45236ASNMET1BB202 - 239202 - 239
46236ASNMET1DD202 - 239202 - 239
47246GLYPRO6BB240 - 244240 - 244
48246GLYPRO6DD240 - 244240 - 244
49256SERVAL1BB245 - 246245 - 246
50256SERVAL1DD245 - 246245 - 246
51266GLUGLU2BB247247
52266GLUGLU2DD247247
53276LEUHIS1BB248 - 265248 - 265
54276LEUHIS1DD248 - 265248 - 265
55286LYSLYS2BB266266
56286LYSLYS2DD266266
57296THRPRO1BB267 - 303267 - 303
58296THRPRO1DD267 - 303267 - 303
59306PROPRO4BB314314
60306PROPRO4DD314314
61316LYSLYS1BB315 - 347315 - 347
62316LYSLYS1DD315 - 347315 - 347
63326ASNARG2BB348 - 358348 - 358
64326ASNARG2DD348 - 358348 - 358
65336THRARG1BB359 - 374359 - 374
66336THRARG1DD359 - 374359 - 374
67346LYSLYS2BB375375
68346LYSLYS2DD375375
69356ALAVAL1BB376 - 412376 - 412
70356ALAVAL1DD376 - 412376 - 412
71366LEULEU3BB1212
72366LEULEU3DD1212
73376VALSER1BB13 - 2813 - 28
74376VALSER1DD13 - 2813 - 28
75386GLYTRP4BB413 - 414413 - 414
76386GLYTRP4DD413 - 414413 - 414

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Transcobalamin II / Transcobalamin / TCII / TC II


Mass: 46315.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TCN2, TC2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168 / References: UniProt: Q9XSC9
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2002
RadiationMonochromator: DOUBLE CRYSTAL (SI111, SI220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2→18 Å / Num. obs: 121830 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.522 / % possible all: 93.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA

Resolution: 2→18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.347 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 4895 4 %RANDOM
Rwork0.241 ---
obs0.243 116949 96.8 %-
all-116949 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20.27 Å2
2---1.06 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13016 0 368 764 14148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3552.02118676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99651652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02423.81588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.727152400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.69715104
X-RAY DIFFRACTIONr_chiral_restr0.0930.22072
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.26156
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.29206
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2766
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.2173
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7891.58272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.489213308
X-RAY DIFFRACTIONr_scbond_it1.95335428
X-RAY DIFFRACTIONr_scangle_it3.1924.55368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2868tight positional0.020.05
2C2909tight positional0.020.05
3A2751tight positional0.030.05
4A2747tight positional0.030.05
5B2751tight positional0.030.05
6B2747tight positional0.030.05
1A192medium positional0.580.5
2C154medium positional0.550.5
3A199medium positional0.630.5
4A199medium positional0.680.5
5B199medium positional0.590.5
6B199medium positional0.660.5
1A194loose positional1.365
2C125loose positional3.025
3A231loose positional2.835
4A235loose positional2.335
5B231loose positional2.835
6B235loose positional2.365
1A2868tight thermal0.060.5
2C2909tight thermal0.060.5
3A2751tight thermal0.080.5
4A2747tight thermal0.080.5
5B2751tight thermal0.080.5
6B2747tight thermal0.080.5
1A192medium thermal0.342
2C154medium thermal0.312
3A199medium thermal0.452
4A199medium thermal0.462
5B199medium thermal0.442
6B199medium thermal0.452
1A194loose thermal0.6710
2C125loose thermal0.4810
3A231loose thermal1.3910
4A235loose thermal1.2610
5B231loose thermal1.4610
6B235loose thermal1.3510
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 335 -
Rwork0.336 8222 -
obs--93.14 %
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)
14.78511.21660.82527.242-0.31772.74490.04660.08520.1631-0.23010.02030.37550.01550.0081-0.0669-0.0251-0.00050.0075-0.02340.0207-0.011532.64675.396738.8917
21.02590.2099-0.03151.6301-0.50310.8818-0.01460.0632-0.0566-0.15610.03260.07020.0155-0.0318-0.018-0.036-0.01820.0093-0.04010.0111-0.063933.8708-7.058634.098
313.433311.70922.4263109.4729-0.04730.4853-0.1089-0.2162-0.93932.9830.9838-5.34030.2607-0.5764-0.87490.0025-0.0001-0.0030.0010.00070.005362.05437.621550.4473
41.75720.1683-0.10133.94781.4821.255-0.0631-0.03140.20270.07680.02350.12040.0245-0.04990.0396-0.02230.00830.0069-0.0913-0.0175-0.034736.484717.794646.4296
56.304-0.37970.061310.2082-0.65012.40920.09940.02580.1818-0.114-0.01850.40560.0516-0.0391-0.0809-0.0012-0.00770.006-0.03680.0116-0.02780.516721.499238.9331
61.14430.2712-0.00571.5001-0.44221.0397-0.00730.0664-0.0199-0.08850.02730.0826-0.0028-0.0011-0.02-0.0455-0.01110.0157-0.05450.005-0.058381.80029.090334.0565
728.673616.81453.235447.7441-3.48681.1303-0.02440.1126-1.90940.35911.5925-7.738-0.0623-0.6761-1.56810.00290.0021-0.00070.001-0.00230.0074110.513823.97250.5807
82.0510.5143-0.19983.29520.96651.2912-0.0635-0.02660.26940.08440.05420.1012-0.0235-0.04130.00930.00020.02070.0064-0.0947-0.0251-0.003184.30133.867946.5403
92.49260.8558-0.027511.3342-0.17643.0656-0.0377-0.00950.0525-0.17710.12930.80120.0438-0.0649-0.0916-0.01-0.0006-0.007-0.02560.0021-0.011238.680432.769310.0679
101.2317-0.3828-0.04681.9185-0.35851.2114-0.01840.02490.0567-0.050.07140.14230.0429-0.033-0.053-0.0632-0.0014-0.0148-0.03980.0028-0.048839.933344.843215.38
1112.850931.2358-0.6653102.1298-15.56237.45491.79910.35880.1954-2.0184-2.83880.47810.1014-0.05161.03970.0035-0.0045-0.0010.00210.00090.001466.806631.8949-2.4913
121.89860.0590.24953.55061.161.4267-0.04550.0747-0.11-0.23530.05130.0711-0.0005-0.0237-0.00590.0364-0.0151-0.005-0.0779-0.0154-0.078642.589820.64432.1811
133.35120.3494-0.33178.60530.94054.37630.0096-0.03010.01750.10490.01510.5025-0.03440.0305-0.0247-0.032-0.0041-0.0084-0.0250.00310.001386.664148.865610.0917
141.1027-0.24550.02731.3722-0.36231.0382-0.03270.02670.05750.01460.03080.11710.0338-0.05510.0018-0.04670.006-0.0072-0.0326-0.0019-0.042187.767461.138615.3655
158.5571-20.7319-1.1183291.518317.04810.99820.21960.2250.4845-5.24660.8665-6.7402-0.6593-0.5262-1.08610.00730.00070.00450.0035-0.00380.0065115.128247.8107-0.3855
161.14340.37510.45634.0561.3341.4676-0.00450.0626-0.0874-0.0878-0.02890.113-0.0438-0.04590.0334-0.0186-0.0027-0.005-0.0667-0.0236-0.048390.590236.73452.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AI01
2X-RAY DIFFRACTION2AA1 - 3021 - 302
3X-RAY DIFFRACTION3AA303 - 314303 - 314
4X-RAY DIFFRACTION4AA315 - 414315 - 414
5X-RAY DIFFRACTION5BJ01
6X-RAY DIFFRACTION6BB1 - 3021 - 302
7X-RAY DIFFRACTION7BB303 - 314303 - 314
8X-RAY DIFFRACTION8BB315 - 414315 - 414
9X-RAY DIFFRACTION9CK01
10X-RAY DIFFRACTION10CC1 - 3021 - 302
11X-RAY DIFFRACTION11CC303 - 314303 - 314
12X-RAY DIFFRACTION12CC315 - 414315 - 414
13X-RAY DIFFRACTION13DL01
14X-RAY DIFFRACTION14DD1 - 3021 - 302
15X-RAY DIFFRACTION15DD303 - 314303 - 314
16X-RAY DIFFRACTION16DD315 - 414315 - 414

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