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- PDB-3cus: Structure of a double ILE/PHE mutant of NI-FE hydrogenase refined... -

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Basic information

Entry
Database: PDB / ID: 3cus
TitleStructure of a double ILE/PHE mutant of NI-FE hydrogenase refined at 2.2 angstrom resolution
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / NI-FE hydrogenase tunnel mutant / Iron / Iron-sulfur / Metal-binding / Nickel
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio fructosovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVolbeda, A.
Citation
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics
Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C.
#2: Journal: Int.J.Hydrogen Energy / Year: 2002
Title: High-Resolution Crystallographic Analysis of Desulfovibrio Fructosovorans [Nife] Hydrogenase
Authors: Volbeda, A. / Montet, Y. / Vernede, X. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#3: Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
History
DepositionApr 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,66529
Polymers264,5516
Non-polymers4,11423
Water18,2491013
1
A: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67811
Polymers88,1842
Non-polymers1,4949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-122.5 kcal/mol
Surface area25290 Å2
MethodPISA
2
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4949
Polymers88,1842
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-121.2 kcal/mol
Surface area25350 Å2
MethodPISA
3
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4949
Polymers88,1842
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-121.2 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.400, 99.960, 182.690
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C
161A
171B
181C
191A
201B
211C
221A
231B
241C
251A
261B
271C
281A
291B
301C
311A
321B
331C
341A
351B
361C
371A
381B
391C
401A
411B
421C
431A
441B
451C
461A
471B
481C
491A
501B
511C
521A
531B
541C
551A
561B
571C
581A
591B
601C
611A
621B
631C
641A
651B
661C
671A
681B
691C
701A
711B
721C
731A
741B
751C
761A
771B
781C
791A
801B
811C
821A
831B
841C
851A
861B
871C
881A
891B
901C
911A
921B
931C
941A
951B
961C
971A
981B
991C
1001A
1011B
1021C
1031A
1041B
1051C
1061A
1071B
1081C
1091A
1101B
1111C
1121A
1131B
1141C
12A
22B
32C
42A
52B
62C
72A
82B
92C
102A
112B
122C
132A
142B
152C
162A
172B
182C
192A
202B
212C
222A
232B
242C
252A
262B
272C
282A
292B
302C
312A
322B
332C
342A
352B
362C
372A
382B
392C
402A
412B
422C
432A
442B
452C
462A
472B
482C
492A
502B
512C
522A
532B
542C
552A
562B
572C
582A
592B
602C
612A
622B
632C
642A
652B
662C
672A
682B
692C
702A
712B
722C
732A
742B
752C
762A
772B
782C
792A
802B
812C
822A
832B
842C
852A
862B
872C
13Q
23R
33S
43Q
53R
63S
73Q
83R
93S
103Q
113R
123S
133Q
143R
153S
163Q
173R
183S
193Q
203R
213S
223Q
233R
243S
253Q
263R
273S
283Q
293R
303S
313Q
323R
333S
343Q
353R
363S
373Q
383R
393S
403Q
413R
423S
433Q
443R
453S
463Q
473R
483S
493Q
503R
513S
523Q
533R
543S
553Q
563R
573S
583Q
593R
603S
613Q
623R
633S
643Q
653R
663S
673Q
683R
693S
703Q
713R
723S
733Q
743R
753S
763Q
773R
783S
793Q
803R
813S
823Q
833R
843S
853Q
863R
873S
883Q
893R
903S
913Q
923R
933S
943Q
953R
963S
973Q
983R
993S
1003Q
1013R
1023S
1033Q
1043R
1053S
1063Q
1073R
1083S
14Q
24R
34S
44Q
54R
64S
74Q
84R
94S
104Q
114R
124S
134Q
144R
154S
164Q
174R
184S
194Q
204R
214S
224Q
234R
244S
254Q
264R
274S
284Q
294R
304S
314Q
324R
334S
344Q
354R
364S
374Q
384R
394S
404Q
414R
424S
434Q
444R
454S
464Q
474R
484S
494Q
504R
514S
524Q
534R
544S
554Q
564R
574S
584Q
594R
604S
614Q
624R
634S
644Q
654R
664S

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROPROPRO3AA77
211PROPROPROPRO3BC77
311PROPROPROPRO3CE77
421SERSERILEILE1AA8 - 288 - 28
521SERSERILEILE1BC8 - 288 - 28
621SERSERILEILE1CE8 - 288 - 28
731LYSLYSPROPRO3AA29 - 3029 - 30
831LYSLYSPROPRO3BC29 - 3029 - 30
931LYSLYSPROPRO3CE29 - 3029 - 30
1041TYRTYRILEILE1AA31 - 3631 - 36
1141TYRTYRILEILE1BC31 - 3631 - 36
1241TYRTYRILEILE1CE31 - 3631 - 36
1351LEULEUTHRTHR3AA37 - 3937 - 39
1451LEULEUTHRTHR3BC37 - 3937 - 39
1551LEULEUTHRTHR3CE37 - 3937 - 39
1661ILEILEGLYGLY1AA40 - 5340 - 53
1761ILEILEGLYGLY1BC40 - 5340 - 53
1861ILEILEGLYGLY1CE40 - 5340 - 53
1971GLUGLUGLUGLU3AA5454
2071GLUGLUGLUGLU3BC5454
2171GLUGLUGLUGLU3CE5454
2281ALAALAALAALA4AA5555
2381ALAALAALAALA4BC5555
2481ALAALAALAALA4CE5555
2591ALAALAGLUGLU1AA56 - 5756 - 57
2691ALAALAGLUGLU1BC56 - 5756 - 57
2791ALAALAGLUGLU1CE56 - 5756 - 57
28101ALAALAALAALA4AA5858
29101ALAALAALAALA4BC5858
30101ALAALAALAALA4CE5858
31111ALAALALEULEU1AA59 - 6059 - 60
32111ALAALALEULEU1BC59 - 6059 - 60
33111ALAALALEULEU1CE59 - 6059 - 60
34121GLNGLNGLNGLN2AA6262
35121GLNGLNGLNGLN2BC6262
36121GLNGLNGLNGLN2CE6262
37131ALAALALEULEU1AA63 - 6463 - 64
38131ALAALALEULEU1BC63 - 6463 - 64
39131ALAALALEULEU1CE63 - 6463 - 64
40141GLUGLUASPASP3AA65 - 6865 - 68
41141GLUGLUASPASP3BC65 - 6865 - 68
42141GLUGLUASPASP3CE65 - 6865 - 68
43151GLYGLYTYRTYR1AA69 - 7069 - 70
44151GLYGLYTYRTYR1BC69 - 7069 - 70
45151GLYGLYTYRTYR1CE69 - 7069 - 70
46161TYRTYRTYRTYR2AA7171
47161TYRTYRTYRTYR2BC7171
48161TYRTYRTYRTYR2CE7171
49171LEULEUILEILE1AA72 - 8172 - 81
50171LEULEUILEILE1BC72 - 8172 - 81
51171LEULEUILEILE1CE72 - 8172 - 81
52181ASPASPGLNGLN3AA82 - 8582 - 85
53181ASPASPGLNGLN3BC82 - 8582 - 85
54181ASPASPGLNGLN3CE82 - 8582 - 85
55191TRPTRPGLYGLY1AA86 - 9186 - 91
56191TRPTRPGLYGLY1BC86 - 9186 - 91
57191TRPTRPGLYGLY1CE86 - 9186 - 91
58201HISHISHISHIS3AA9292
59201HISHISHISHIS3BC9292
60201HISHISHISHIS3CE9292
61211PROPROMETMET1AA93 - 9493 - 94
62211PROPROMETMET1BC93 - 9493 - 94
63211PROPROMETMET1CE93 - 9493 - 94
64221ILEILELYSLYS3AA95 - 9995 - 99
65221ILEILELYSLYS3BC95 - 9995 - 99
66221ILEILELYSLYS3CE95 - 9995 - 99
67231ALAALAALAALA1AA101101
68231ALAALAALAALA1BC101101
69231ALAALAALAALA1CE101101
70241LYSLYSLYSLYS3AA104104
71241LYSLYSLYSLYS3BC104104
72241LYSLYSLYSLYS3CE104104
73251ALAALAALAALA4AA105105
74251ALAALAALAALA4BC105105
75251ALAALAALAALA4CE105105
76261LYSLYSLYSLYS3AA106106
77261LYSLYSLYSLYS3BC106106
78261LYSLYSLYSLYS3CE106106
79271GLYGLYALAALA1AA107 - 130107 - 130
80271GLYGLYALAALA1BC107 - 130107 - 130
81271GLYGLYALAALA1CE107 - 130107 - 130
82281LYSLYSLYSLYS2AA131131
83281LYSLYSLYSLYS2BC131131
84281LYSLYSLYSLYS2CE131131
85291GLYGLYVALVAL1AA132 - 133132 - 133
86291GLYGLYVALVAL1BC132 - 133132 - 133
87291GLYGLYVALVAL1CE132 - 133132 - 133
88301THRTHRVALVAL1AA141 - 159141 - 159
89301THRTHRVALVAL1BC141 - 159141 - 159
90301THRTHRVALVAL1CE141 - 159141 - 159
91311HISHISHISHIS2AA160160
92311HISHISHISHIS2BC160160
93311HISHISHISHIS2CE160160
94321VALVALLEULEU3AA161 - 162161 - 162
95321VALVALLEULEU3BC161 - 162161 - 162
96321VALVALLEULEU3CE161 - 162161 - 162
97331THRTHRTHRTHR6AA163163
98331THRTHRTHRTHR6BC163163
99331THRTHRTHRTHR6CE163163
100341LYSLYSLYSLYS3AA164164
101341LYSLYSLYSLYS3BC164164
102341LYSLYSLYSLYS3CE164164
103351GLYGLYPROPRO2AA165 - 167165 - 167
104351GLYGLYPROPRO2BC165 - 167165 - 167
105351GLYGLYPROPRO2CE165 - 167165 - 167
106361ASPASPLEULEU3AA168 - 169168 - 169
107361ASPASPLEULEU3BC168 - 169168 - 169
108361ASPASPLEULEU3CE168 - 169168 - 169
109371ASPASPGLUGLU6AA170 - 171170 - 171
110371ASPASPGLUGLU6BC170 - 171170 - 171
111371ASPASPGLUGLU6CE170 - 171170 - 171
112381SF4SF4SF4SF41AI267
113381SF4SF4SF4SF41BR267
114381SF4SF4SF4SF41CY267
112GLYGLYPROPRO1AA173 - 175173 - 175
212GLYGLYPROPRO1BC173 - 175173 - 175
312GLYGLYPROPRO1CE173 - 175173 - 175
422LYSLYSLEULEU3AA176 - 177176 - 177
522LYSLYSLEULEU3BC176 - 177176 - 177
622LYSLYSLEULEU3CE176 - 177176 - 177
732PHEPHETYRTYR1AA178 - 179178 - 179
832PHEPHETYRTYR1BC178 - 179178 - 179
932PHEPHETYRTYR1CE178 - 179178 - 179
1042GLYGLYLEULEU3AA180 - 182180 - 182
1142GLYGLYLEULEU3BC180 - 182180 - 182
1242GLYGLYLEULEU3CE180 - 182180 - 182
1352VALVALCYSCYS1AA183 - 187183 - 187
1452VALVALCYSCYS1BC183 - 187183 - 187
1552VALVALCYSCYS1CE183 - 187183 - 187
1662PROPROLEULEU2AA188 - 190188 - 190
1762PROPROLEULEU2BC188 - 190188 - 190
1862PROPROLEULEU2CE188 - 190188 - 190
1972PROPROGLUGLU3AA191 - 194191 - 194
2072PROPROGLUGLU3BC191 - 194191 - 194
2172PROPROGLUGLU3CE191 - 194191 - 194
2282ALAALASERSER2AA195 - 196195 - 196
2382ALAALASERSER2BC195 - 196195 - 196
2482ALAALASERSER2CE195 - 196195 - 196
2592GLUGLUPHEPHE3AA197 - 198197 - 198
2692GLUGLUPHEPHE3BC197 - 198197 - 198
2792GLUGLUPHEPHE3CE197 - 198197 - 198
28102ALAALAPHEPHE1AA199 - 202199 - 202
29102ALAALAPHEPHE1BC199 - 202199 - 202
30102ALAALAPHEPHE1CE199 - 202199 - 202
31112ASPASPASPASP3AA203203
32112ASPASPASPASP3BC203203
33112ASPASPASPASP3CE203203
34122SERSERSERSER1AA204204
35122SERSERSERSER1BC204204
36122SERSERSERSER1CE204204
37132GLUGLUGLUGLU3AA205 - 206205 - 206
38132GLUGLUGLUGLU3BC205 - 206205 - 206
39132GLUGLUGLUGLU3CE205 - 206205 - 206
40142ALAALALYSLYS1AA207 - 208207 - 208
41142ALAALALYSLYS1BC207 - 208207 - 208
42142ALAALALYSLYS1CE207 - 208207 - 208
43152LYSLYSLYSLYS3AA209209
44152LYSLYSLYSLYS3BC209209
45152LYSLYSLYSLYS3CE209209
46162GLYGLYLEULEU1AA210 - 213210 - 213
47162GLYGLYLEULEU1BC210 - 213210 - 213
48162GLYGLYLEULEU1CE210 - 213210 - 213
49172TYRTYRGLUGLU3AA214 - 215214 - 215
50172TYRTYRGLUGLU3BC214 - 215214 - 215
51172TYRTYRGLUGLU3CE214 - 215214 - 215
52182LEULEUGLYGLY1AA216 - 220216 - 220
53182LEULEUGLYGLY1BC216 - 220216 - 220
54182LEULEUGLYGLY1CE216 - 220216 - 220
55192PROPROPROPRO2AA221221
56192PROPROPROPRO2BC221221
57192PROPROPROPRO2CE221221
58202VALVALPROPRO1AA222 - 228222 - 228
59202VALVALPROPRO1BC222 - 228222 - 228
60202VALVALPROPRO1CE222 - 228222 - 228
61212LYSLYSLYSLYS3AA229229
62212LYSLYSLYSLYS3BC229229
63212LYSLYSLYSLYS3CE229229
64222VALVALASNASN1AA230 - 233230 - 233
65222VALVALASNASN1BC230 - 233230 - 233
66222VALVALASNASN1CE230 - 233230 - 233
67232GLNGLNGLNGLN2AA234234
68232GLNGLNGLNGLN2BC234234
69232GLNGLNGLNGLN2CE234234
70242VALVALTRPTRP1AA235 - 254235 - 254
71242VALVALTRPTRP1BC235 - 254235 - 254
72242VALVALTRPTRP1CE235 - 254235 - 254
73252ASPASPASPASP4AA255255
74252ASPASPASPASP4BC255255
75252ASPASPASPASP4CE255255
76262THRTHRTHRTHR1AA256 - 258256 - 258
77262THRTHRTHRTHR1BC256 - 258256 - 258
78262THRTHRTHRTHR1CE256 - 258256 - 258
79272PROPROPROPRO2AA259259
80272PROPROPROPRO2BC259259
81272PROPROPROPRO2CE259259
82282PHEPHETYRTYR1AA260 - 261260 - 261
83282PHEPHETYRTYR1BC260 - 261260 - 261
84282PHEPHETYRTYR1CE260 - 261260 - 261
85292SF4SF4F3SF3S1AG - H265 - 266
86292SF4SF4F3SF3S1BP - Q265 - 266
87292SF4SF4F3SF3S1CW - X265 - 266
113THRTHRGLYGLY3QB7 - 147 - 14
213THRTHRGLYGLY3RD7 - 147 - 14
313THRTHRGLYGLY3SF7 - 147 - 14
423PROPROVALVAL1QB15 - 3215 - 32
523PROPROVALVAL1RD15 - 3215 - 32
623PROPROVALVAL1SF15 - 3215 - 32
733GLUGLULYSLYS3QB33 - 4033 - 40
833GLUGLULYSLYS3RD33 - 4033 - 40
933GLUGLULYSLYS3SF33 - 4033 - 40
1043ASPASPLEULEU1QB41 - 5641 - 56
1143ASPASPLEULEU1RD41 - 5641 - 56
1243ASPASPLEULEU1SF41 - 5641 - 56
1353LYSLYSLYSLYS3QB5757
1453LYSLYSLYSLYS3RD5757
1553LYSLYSLYSLYS3SF5757
1663GLYGLYPROPRO1QB58 - 6158 - 61
1763GLYGLYPROPRO1RD58 - 6158 - 61
1863GLYGLYPROPRO1SF58 - 6158 - 61
1973ARGARGARGARG3QB6262
2073ARGARGARGARG3RD6262
2173ARGARGARGARG3SF6262
2283GLYGLYVALVAL1QB58 - 9158 - 91
2383GLYGLYVALVAL1RD58 - 9158 - 91
2483GLYGLYVALVAL1SF58 - 9158 - 91
2593LYSLYSSERSER3QB92 - 9492 - 94
2693LYSLYSSERSER3RD92 - 9492 - 94
2793LYSLYSSERSER3SF92 - 9492 - 94
28103ILEILEHISHIS1QB95 - 11595 - 115
29103ILEILEHISHIS1RD95 - 11595 - 115
30103ILEILEHISHIS1SF95 - 11595 - 115
31113LEULEULEULEU3QB116116
32113LEULEULEULEU3RD116116
33113LEULEULEULEU3SF116116
34123VALVALVALVAL1QB117 - 130117 - 130
35123VALVALVALVAL1RD117 - 130117 - 130
36123VALVALVALVAL1SF117 - 130117 - 130
37133THRTHRALAALA5QB131 - 133131 - 133
38133THRTHRALAALA5RD131 - 133131 - 133
39133THRTHRALAALA5SF131 - 133131 - 133
40143ALAALAALAALA4QB141 - 142141 - 142
41143ALAALAALAALA4RD141 - 142141 - 142
42143ALAALAALAALA4SF141 - 142141 - 142
43153ALAALAALAALA3QB151 - 159151 - 159
44153ALAALAALAALA3RD151 - 159151 - 159
45153ALAALAALAALA3SF151 - 159151 - 159
46163LYSLYSLEULEU3QB161 - 176161 - 176
47163LYSLYSLEULEU3RD161 - 176161 - 176
48163LYSLYSLEULEU3SF161 - 176161 - 176
49173GLYGLYTHRTHR1QB177 - 180177 - 180
50173GLYGLYTHRTHR1RD177 - 180177 - 180
51173GLYGLYTHRTHR1SF177 - 180177 - 180
52183ASNASNLEULEU3QB181 - 185181 - 185
53183ASNASNLEULEU3RD181 - 185181 - 185
54183ASNASNLEULEU3SF181 - 185181 - 185
55193ALAALAGLUGLU3QB190 - 196190 - 196
56193ALAALAGLUGLU3RD190 - 196190 - 196
57193ALAALAGLUGLU3SF190 - 196190 - 196
58203VALVALTYRTYR1QB197 - 205197 - 205
59203VALVALTYRTYR1RD197 - 205197 - 205
60203VALVALTYRTYR1SF197 - 205197 - 205
61213LEULEULYSLYS2QB206 - 214206 - 214
62213LEULEULYSLYS2RD206 - 214206 - 214
63213LEULEULYSLYS2SF206 - 214206 - 214
64223ALAALATYRTYR1QB215 - 240215 - 240
65223ALAALATYRTYR1RD215 - 240215 - 240
66223ALAALATYRTYR1SF215 - 240215 - 240
67233GLNGLNLYSLYS3QB241 - 278241 - 278
68233GLNGLNLYSLYS3RD241 - 278241 - 278
69233GLNGLNLYSLYS3SF241 - 278241 - 278
70243ALAALATHRTHR2QB415 - 421415 - 421
71243ALAALATHRTHR2RD415 - 421415 - 421
72243ALAALATHRTHR2SF415 - 421415 - 421
73253LEULEULEULEU3QB422422
74253LEULEULEULEU3RD422422
75253LEULEULEULEU3SF422422
76263GLYGLYMETMET1QB423 - 439423 - 439
77263GLYGLYMETMET1RD423 - 439423 - 439
78263GLYGLYMETMET1SF423 - 439423 - 439
79273GLUGLUMETMET3QB440 - 446440 - 446
80273GLUGLUMETMET3RD440 - 446440 - 446
81273GLUGLUMETMET3SF440 - 446440 - 446
82283LEULEULYSLYS3QB456 - 467456 - 467
83283LEULEULYSLYS3RD456 - 467456 - 467
84283LEULEULYSLYS3SF456 - 467456 - 467
85293GLYGLYILEILE1QB468 - 483468 - 483
86293GLYGLYILEILE1RD468 - 483468 - 483
87293GLYGLYILEILE1SF468 - 483468 - 483
88303ARGARGASNASN3QB484 - 492484 - 492
89303ARGARGASNASN3RD484 - 492484 - 492
90303ARGARGASNASN3SF484 - 492484 - 492
91313PHEPHEPROPRO1QB493 - 505493 - 505
92313PHEPHEPROPRO1RD493 - 505493 - 505
93313PHEPHEPROPRO1SF493 - 505493 - 505
94323ARGARGILEILE3QB506 - 520506 - 520
95323ARGARGILEILE3RD506 - 520506 - 520
96323ARGARGILEILE3SF506 - 520506 - 520
97333GLYGLYALAALA1QB521 - 525521 - 525
98333GLYGLYALAALA1RD521 - 525521 - 525
99333GLYGLYALAALA1SF521 - 525521 - 525
100343PROPROILEILE1QB530 - 533530 - 533
101343PROPROILEILE1RD530 - 533530 - 533
102343PROPROILEILE1SF530 - 533530 - 533
103353LEULEUHISHIS1QB534 - 549534 - 549
104353LEULEUHISHIS1RD534 - 549534 - 549
105353LEULEUHISHIS1SF534 - 549534 - 549
106363FCOFCOMGMG1QM - L550 - 553
107363FCOFCOMGMG1RU - T550 - 553
108363FCOFCOMGMG1SBA - AA550 - 553
114ASPASPASPASP3QB279279
214ASPASPASPASP3RD279279
314ASPASPASPASP3SF279279
424TRPTRPTHRTHR1QB280 - 286280 - 286
524TRPTRPTHRTHR1RD280 - 286280 - 286
624TRPTRPTHRTHR1SF280 - 286280 - 286
734SERSERASNASN2QB287 - 288287 - 288
834SERSERASNASN2RD287 - 288287 - 288
934SERSERASNASN2SF287 - 288287 - 288
1044TYRTYRASPASP1QB289 - 299289 - 299
1144TYRTYRASPASP1RD289 - 299289 - 299
1244TYRTYRASPASP1SF289 - 299289 - 299
1354SERSERPROPRO1QB301 - 302301 - 302
1454SERSERPROPRO1RD301 - 302301 - 302
1554SERSERPROPRO1SF301 - 302301 - 302
1664LYSLYSGLYGLY1QB304 - 318304 - 318
1764LYSLYSGLYGLY1RD304 - 318304 - 318
1864LYSLYSGLYGLY1SF304 - 318304 - 318
1974ARGARGLEULEU3QB319 - 329319 - 329
2074ARGARGLEULEU3RD319 - 329319 - 329
2174ARGARGLEULEU3SF319 - 329319 - 329
2284ALAALALYSLYS3QB331 - 337331 - 337
2384ALAALALYSLYS3RD331 - 337331 - 337
2484ALAALALYSLYS3SF331 - 337331 - 337
2594TYRTYRTYRTYR2QB338 - 341338 - 341
2694TYRTYRTYRTYR2RD338 - 341338 - 341
2794TYRTYRTYRTYR2SF338 - 341338 - 341
28104GLYGLYGLYGLY4QB345345
29104GLYGLYGLYGLY4RD345345
30104GLYGLYGLYGLY4SF345345
31114ASPASPLYSLYS3QB346 - 348346 - 348
32114ASPASPLYSLYS3RD346 - 348346 - 348
33114ASPASPLYSLYS3SF346 - 348346 - 348
34124HISHISTYRTYR2QB349 - 351349 - 351
35124HISHISTYRTYR2RD349 - 351349 - 351
36124HISHISTYRTYR2SF349 - 351349 - 351
37134ASPASPTYRTYR3QB352 - 359352 - 359
38134ASPASPTYRTYR3RD352 - 359352 - 359
39134ASPASPTYRTYR3SF352 - 359352 - 359
40144LYSLYSHISHIS3QB365 - 367365 - 367
41144LYSLYSHISHIS3RD365 - 367365 - 367
42144LYSLYSHISHIS3SF365 - 367365 - 367
43154TYRTYRTYRTYR1QB368 - 376368 - 376
44154TYRTYRTYRTYR1RD368 - 376368 - 376
45154TYRTYRTYRTYR1SF368 - 376368 - 376
46164ALAALAALAALA1QB380 - 392380 - 392
47164ALAALAALAALA1RD380 - 392380 - 392
48164ALAALAALAALA1SF380 - 392380 - 392
49174TYRTYRTYRTYR2QB393393
50174TYRTYRTYRTYR2RD393393
51174TYRTYRTYRTYR2SF393393
52184ALAALALYSLYS3QB394 - 395394 - 395
53184ALAALALYSLYS3RD394 - 395394 - 395
54184ALAALALYSLYS3SF394 - 395394 - 395
55194GLYGLYPHEPHE2QB396 - 400396 - 400
56194GLYGLYPHEPHE2RD396 - 400396 - 400
57194GLYGLYPHEPHE2SF396 - 400396 - 400
58204LYSLYSLYSLYS3QB401401
59204LYSLYSLYSLYS3RD401401
60204LYSLYSLYSLYS3SF401401
61214VALVALLEULEU5QB407 - 408407 - 408
62214VALVALLEULEU5RD407 - 408407 - 408
63214VALVALLEULEU5SF407 - 408407 - 408
64224LEULEUPROPRO3QB411 - 414411 - 414
65224LEULEUPROPRO3RD411 - 414411 - 414
66224LEULEUPROPRO3SF411 - 414411 - 414

NCS ensembles :
ID
1
2
3
4

-
Components

-
Periplasmic [NiFe] hydrogenase ... , 2 types, 6 molecules ABCQRS

#1: Protein Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28347.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio fructosovorans (bacteria)
Strain: wild type / Gene: hydA / Production host: Desulfovibrio fructosovorans (bacteria) / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59836.375 Da / Num. of mol.: 3 / Mutation: V74I, L122F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio fructosovorans (bacteria)
Strain: wild type / Gene: hydB / Production host: Desulfovibrio fructosovorans (bacteria) / References: UniProt: P18188, cytochrome-c3 hydrogenase

-
Non-polymers , 7 types, 1036 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1013 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, GLYCEROL, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9341
ReflectionResolution: 2.18→20 Å / Num. all: 115860 / Num. obs: 108157 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.3 / Num. unique all: 17163 / Rsym value: 0.198 / % possible all: 71

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW
Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.41 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.387 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22223 5404 5 %RANDOM
Rwork0.18493 ---
obs0.18677 101754 94.24 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.032 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20.21 Å2
2---0.93 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18418 0 126 1013 19557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02219146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.96525958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5215.0252417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16224.413775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12153040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5431572
X-RAY DIFFRACTIONr_chiral_restr0.0850.22826
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.29498
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.212921
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21358
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4011.512431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.602319307
X-RAY DIFFRACTIONr_scbond_it0.7227778
X-RAY DIFFRACTIONr_scangle_it1.0944.56570
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
11A951tight positional0.050.06
12B951tight positional0.040.06
13C951tight positional0.050.06
21A603tight positional0.040.06
22B603tight positional0.040.06
23C603tight positional0.050.06
31Q2297tight positional0.050.06
32R2297tight positional0.050.06
33S2297tight positional0.050.06
41Q653tight positional0.050.06
42R653tight positional0.050.06
43S653tight positional0.050.06
11A46medium positional0.260.2
12B46medium positional0.250.2
13C46medium positional0.470.2
21A36medium positional0.110.2
22B36medium positional0.10.2
23C36medium positional0.10.2
31Q79medium positional0.140.2
32R79medium positional0.120.2
33S79medium positional0.130.2
41Q90medium positional0.110.2
42R90medium positional0.10.2
43S90medium positional0.120.2
11A126loose positional0.415
12B126loose positional0.575
13C126loose positional0.425
21A88loose positional0.295
22B88loose positional0.395
23C88loose positional0.375
31Q532loose positional0.445
32R532loose positional0.445
33S532loose positional0.525
41Q160loose positional0.435
42R160loose positional0.355
43S160loose positional0.435
11A951tight thermal0.291
12B951tight thermal0.271
13C951tight thermal0.281
21A603tight thermal0.321
22B603tight thermal0.311
23C603tight thermal0.271
31Q2297tight thermal0.31
32R2297tight thermal0.281
33S2297tight thermal0.271
41Q653tight thermal0.311
42R653tight thermal0.251
43S653tight thermal0.271
11A46medium thermal0.582
12B46medium thermal0.482
13C46medium thermal0.552
21A36medium thermal0.592
22B36medium thermal0.62
23C36medium thermal0.52
31Q79medium thermal0.762
32R79medium thermal0.532
33S79medium thermal0.782
41Q90medium thermal0.662
42R90medium thermal0.612
43S90medium thermal0.482
11A126loose thermal1.5110
12B126loose thermal1.5510
13C126loose thermal1.8310
21A88loose thermal1.310
22B88loose thermal1.4210
23C88loose thermal110
31Q532loose thermal1.1610
32R532loose thermal1.0810
33S532loose thermal1.0310
41Q160loose thermal1.0110
42R160loose thermal1.0410
43S160loose thermal1.0210
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 356 -
Rwork0.222 6639 -
obs--83.9 %

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