[English] 日本語
Yorodumi
- PDB-4uew: Structure of H2-treated anaerobically purified D. fructosovorans ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uew
TitleStructure of H2-treated anaerobically purified D. fructosovorans NiFe- hydrogenase
Components(PERIPLASMIC [NIFE] HYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NIFE-HYDROGENASE / NI-SIB STATE / NI-C STATE
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 / Nickel-dependent hydrogenase large subunit / cytochrome-c3 hydrogenase / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
DESULFOVIBRIO FRUCTOSOVORANS JJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsVolbeda, A. / Martin, L. / Liebgott, P.-P. / Fontecilla-Camps, J.C.
CitationJournal: Metallomics / Year: 2015
Title: [NiFe]-hydrogenases revisited: nickel-carboxamido bond formation in a variant with accrued O2-tolerance and a tentative re-interpretation of Ni-SI states.
Authors: Volbeda, A. / Martin, L. / Liebgott, P.P. / De Lacey, A.L. / Fontecilla-Camps, J.C.
History
DepositionDec 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / exptl_crystal_grow / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
B: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
C: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
Q: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
R: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
S: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,35038
Polymers264,4076
Non-polymers4,94332
Water30,6441701
1
B: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
R: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,90614
Polymers88,1362
Non-polymers1,77112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-122.4 kcal/mol
Surface area25650 Å2
MethodPISA
2
C: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
S: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4469
Polymers88,1362
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-121.7 kcal/mol
Surface area25360 Å2
MethodPISA
3
A: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
Q: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,99815
Polymers88,1362
Non-polymers1,86313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-120.6 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.770, 100.400, 183.430
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C
15A
25B
35C
16A
26B
36C
17A
27B
37C
18Q
28R
38S
19Q
29R
39S
110Q
210R
310S
111Q
211R
311S
112Q
212R
312S
113Q
213R
313S
114Q
214R
314S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A7
2113B7
3113C7
1211A8 - 28
2211B8 - 28
3211C8 - 28
1313A29 - 30
2313B29 - 30
3313C29 - 30
1411A31 - 36
2411B31 - 36
3411C31 - 36
1513A37 - 39
2513B37 - 39
3513C37 - 39
1611A40 - 53
2611B40 - 53
3611C40 - 53
1713A54
2713B54
3713C54
1814A55
2814B55
3814C55
1911A56 - 57
2911B56 - 57
3911C56 - 57
11014A58
21014B58
31014C58
1121A59 - 60
2121B59 - 60
3121C59 - 60
1222A62
2222B62
3222C62
1321A63 - 64
2321B63 - 64
3321C63 - 64
1423A65 - 68
2423B65 - 68
3423C65 - 68
1521A69 - 70
2521B69 - 70
3521C69 - 70
1622A71
2622B71
3622C71
1721A72 - 81
2721B72 - 81
3721C72 - 81
1823A82 - 85
2823B82 - 85
3823C82 - 85
1921A86 - 91
2921B86 - 91
3921C86 - 91
11023A92
21023B92
31023C92
1131A93 - 94
2131B93 - 94
3131C93 - 94
1233A95 - 99
2233B95 - 99
3233C95 - 99
1331A101
2331B101
3331C101
1433A104
2433B104
3433C104
1534A105
2534B105
3534C105
1633A106
2633B106
3633C106
1731A107 - 130
2731B107 - 130
3731C107 - 130
1832A131
2832B131
3832C131
1931A132 - 133
2931B132 - 133
3931C132 - 133
11031A141 - 159
21031B141 - 159
31031C141 - 159
1142A160
2142B160
3142C160
1243A161 - 162
2243B161 - 162
3243C161 - 162
1346A163
2346B163
3346C163
1443A164
2443B164
3443C164
1542A165 - 167
2542B165 - 167
3542C165 - 167
1643A168 - 169
2643B168 - 169
3643C168 - 169
1746A170 - 171
2746B170 - 171
3746C170 - 171
1841A267
2841B267
3841C267
1151A173 - 175
2151B173 - 175
3151C173 - 175
1253A176 - 177
2253B176 - 177
3253C176 - 177
1351A178 - 179
2351B178 - 179
3351C178 - 179
1453A180 - 182
2453B180 - 182
3453C180 - 182
1551A183 - 187
2551B183 - 187
3551C183 - 187
1652A188 - 190
2652B188 - 190
3652C188 - 190
1753A191 - 194
2753B191 - 194
3753C191 - 194
1852A195 - 196
2852B195 - 196
3852C195 - 196
1953A197 - 198
2953B197 - 198
3953C197 - 198
11051A199 - 202
21051B199 - 202
31051C199 - 202
1163A203
2163B203
3163C203
1261A204
2261B204
3261C204
1363A205 - 206
2363B205 - 206
3363C205 - 206
1461A207 - 208
2461B207 - 208
3461C207 - 208
1563A209
2563B209
3563C209
1661A210 - 213
2661B210 - 213
3661C210 - 213
1763A214 - 215
2763B214 - 215
3763C214 - 215
1861A216 - 220
2861B216 - 220
3861C216 - 220
1962A221
2962B221
3962C221
11061A222 - 228
21061B222 - 228
31061C222 - 228
1173A229
2173B229
3173C229
1271A230 - 233
2271B230 - 233
3271C230 - 233
1372A234
2372B234
3372C234
1471A235 - 254
2471B235 - 254
3471C235 - 254
1574A255
2574B255
3574C255
1671A256 - 258
2671B256 - 258
3671C256 - 258
1772A259
2772B259
3772C259
1871A260 - 261
2871B260 - 261
3871C260 - 261
1971A265 - 266
2971B265 - 266
3971C265 - 266
1183Q7 - 14
2183R7 - 14
3183S7 - 14
1281Q15 - 32
2281R15 - 32
3281S15 - 32
1383Q33 - 40
2383R33 - 40
3383S33 - 40
1481Q41 - 56
2481R41 - 56
3481S41 - 56
1583Q57
2583R57
3583S57
1681Q58 - 61
2681R58 - 61
3681S58 - 61
1783Q62
2783R62
3783S62
1881Q58 - 91
2881R58 - 91
3881S58 - 91
1983Q92 - 94
2983R92 - 94
3983S92 - 94
11081Q95 - 115
21081R95 - 115
31081S95 - 115
1193Q116
2193R116
3193S116
1291Q117 - 130
2291R117 - 130
3291S117 - 130
1395Q131 - 133
2395R131 - 133
3395S131 - 133
1494Q141 - 142
2494R141 - 142
3494S141 - 142
1593Q151 - 159
2593R151 - 159
3593S151 - 159
1693Q161 - 176
2693R161 - 176
3693S161 - 176
1791Q177 - 180
2791R177 - 180
3791S177 - 180
1893Q181 - 185
2893R181 - 185
3893S181 - 185
1993Q190 - 196
2993R190 - 196
3993S190 - 196
11091Q197 - 205
21091R197 - 205
31091S197 - 205
11102Q206 - 214
21102R206 - 214
31102S206 - 214
12101Q215 - 240
22101R215 - 240
32101S215 - 240
13103Q241 - 278
23103R241 - 278
33103S241 - 278
14102Q415 - 421
24102R415 - 421
34102S415 - 421
15103Q422
25103R422
35103S422
16101Q423 - 439
26101R423 - 439
36101S423 - 439
17103Q440 - 446
27103R440 - 446
37103S440 - 446
18103Q456 - 467
28103R456 - 467
38103S456 - 467
19101Q468 - 483
29101R468 - 483
39101S468 - 483
110103Q484 - 492
210103R484 - 492
310103S484 - 492
11111Q493 - 505
21111R493 - 505
31111S493 - 505
12113Q506 - 520
22113R506 - 520
32113S506 - 520
13111Q521 - 525
23111R521 - 525
33111S521 - 525
14111Q530 - 533
24111R530 - 533
34111S530 - 533
15111Q534 - 549
25111R534 - 549
35111S534 - 549
16111Q550 - 553
26111R550 - 553
36111S550 - 553
11123Q279
21123R279
31123S279
12121Q280 - 286
22121R280 - 286
32121S280 - 286
13122Q287 - 288
23122R287 - 288
33122S287 - 288
14121Q289 - 299
24121R289 - 299
34121S289 - 299
15121Q301 - 302
25121R301 - 302
35121S301 - 302
16121Q304 - 318
26121R304 - 318
36121S304 - 318
17123Q319 - 329
27123R319 - 329
37123S319 - 329
18123Q331 - 337
28123R331 - 337
38123S331 - 337
19122Q338 - 341
29122R338 - 341
39122S338 - 341
110124Q345
210124R345
310124S345
11133Q346 - 348
21133R346 - 348
31133S346 - 348
12132Q349 - 351
22132R349 - 351
32132S349 - 351
13133Q352 - 359
23133R352 - 359
33133S352 - 359
14133Q365 - 367
24133R365 - 367
34133S365 - 367
15131Q368 - 376
25131R368 - 376
35131S368 - 376
11141Q380 - 392
21141R380 - 392
31141S380 - 392
12142Q393
22142R393
32142S393
13143Q394 - 395
23143R394 - 395
33143S394 - 395
14142Q396 - 400
24142R396 - 400
34142S396 - 400
15143Q401
25143R401
35143S401
16145Q407 - 408
26145R407 - 408
36145S407 - 408
17143Q411 - 414
27143R411 - 414
37143S411 - 414

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(0.38583, -0.741475, 0.548953), (-0.752107, -0.5974, -0.278297), (0.534295, -0.305496, -0.788163)-35.675, -26.93, 54.657
2given(-0.380984, -0.735909, -0.559722), (0.730438, -0.610712, 0.305765), (-0.566844, -0.292351, 0.770207)1.354, 4.237, 69.273
3given(0.382829, -0.740399, 0.552495), (-0.748136, -0.599331, -0.284773), (0.541973, -0.304322, -0.78336)-35.659, -26.877, 54.55
4given(-0.374865, -0.739484, -0.559142), (0.730622, -0.606905, 0.312822), (-0.570673, -0.291256, 0.767791)1.281, 4.174, 69.334
5given(1), (1), (1)
6given(0.382054, -0.751371, 0.53803), (-0.742566, -0.596164, -0.305261), (0.550119, -0.282896, -0.785709)-35.96402, -25.83834, 54.89409
7given(-0.373545, 0.729294, -0.573232), (-0.737488, -0.608321, -0.293354), (-0.56265, 0.31317, 0.765081)37.25006, 23.86848, -53.62646
8given(1), (1), (1)
9given(0.383053, -0.752455, 0.535801), (-0.743311, -0.595457, -0.304827), (0.548415, -0.281502, -0.787399)-35.90758, -25.84453, 55.03253
10given(-0.37258, 0.731467, -0.571087), (-0.737537, -0.606899, -0.296163), (-0.563226, 0.310853, 0.765602)37.17153, 24.0979, -53.55692
11given(1), (1), (1)
12given(0.387456, -0.75034, 0.5356), (-0.742452, -0.598373, -0.301188), (0.546483, -0.28096, -0.788935)-35.59795, -26.10445, 55.02672
13given(-0.377146, 0.731161, -0.568475), (-0.735769, -0.609329, -0.295572), (-0.562499, 0.306792, 0.767772)36.93143, 24.06841, -53.75022
14given(1), (1), (1)
15given(0.391049, -0.746156, 0.538824), (-0.734649, -0.605714, -0.305616), (0.55441, -0.276336, -0.785027)-35.42058, -26.0034, 55.32904
16given(-0.379979, 0.732158, -0.565297), (-0.737264, -0.608798, -0.292928), (-0.558621, 0.305467, 0.771124)36.68073, 23.85812, -53.90741
17given(1), (1), (1)
18given(0.401481, -0.752267, 0.522405), (-0.73771, -0.603649, -0.302311), (0.542768, -0.264011, -0.797309)-34.3078, -26.25784, 56.17042
19given(-0.385647, 0.740277, -0.550696), (-0.739698, -0.604818, -0.295027), (-0.551473, 0.293572, 0.780828)35.7505, 23.81386, -54.18481
20given(1), (1), (1)
21given(0.389684, -0.755362, 0.526854), (-0.74358, -0.595585, -0.303919), (0.543355, -0.273326, -0.793762)-35.12664, -25.99972, 55.55422
22given(-0.382347, 0.734922, -0.56009), (-0.737743, -0.607768, -0.29386), (-0.556369, 0.300846, 0.774562)36.2805, 23.81971, -54.03187
23given(1), (1), (1)
24given(0.386086, -0.753351, 0.532353), (-0.738491, -0.598248, -0.311016), (0.552783, -0.273059, -0.787318)-35.54553, -25.41391, 55.49051
25given(-0.380565, 0.730819, -0.566634), (-0.73846, -0.608994, -0.289486), (-0.556639, 0.308268, 0.771443)36.716, 23.61721, -53.96901
26given(1), (1), (1)
27given(0.383958, -0.74834, 0.540892), (-0.739905, -0.599796, -0.304607), (0.552374, -0.283252, -0.783997)-35.95586, -25.89696, 54.87771
28given(-0.377766, 0.72988, -0.569709), (-0.737155, -0.609405, -0.291939), (-0.560264, 0.309679, 0.768247)36.95549, 23.75672, -53.80813
29given(1), (1), (1)
30given(0.384405, -0.74718, 0.542176), (-0.741281, -0.599863, -0.301108), (0.550213, -0.286158, -0.784461)-35.94498, -26.04287, 54.71978
31given(-0.37385, 0.727169, -0.575727), (-0.737969, -0.609218, -0.290267), (-0.561816, 0.316352, 0.764384)37.51352, 23.77587, -53.61886
32given(1), (1), (1)
33given(0.383806, -0.749077, 0.539979), (-0.739714, -0.599434, -0.305781), (0.552735, -0.28207, -0.784169)-35.9052, -25.81222, 54.8974
34given(-0.374463, 0.730785, -0.570728), (-0.740305, -0.606247, -0.29054), (-0.558324, 0.313717, 0.768021)36.97086, 23.60106, -53.87592
35given(1), (1), (1)
36given(0.381602, -0.748052, 0.542954), (-0.742394, -0.597987, -0.302099), (0.550664, -0.287804, -0.783542)-36.07614, -26.01747, 54.71325
37given(-0.373029, 0.732554, -0.569398), (-0.737892, -0.606267, -0.296574), (-0.562463, 0.309523, 0.766701)36.94576, 24.08813, -53.7212
38given(1), (1), (1)
39given(0.382971, -0.74734, 0.54297), (-0.740191, -0.599925, -0.303656), (0.552676, -0.28561, -0.782928)-35.99257, -25.93536, 54.76598
40given(-0.375395, 0.730636, -0.570306), (-0.739789, -0.606879, -0.290536), (-0.558383, 0.31284, 0.768336)36.96508, 23.57652, -53.89859
41given(1), (1), (1)
42given(0.384643, -0.742734, 0.548084), (-0.738695, -0.603731, -0.299731), (0.553516, -0.289577, -0.780875)-36.15726, -26.10934, 54.62579
43given(-0.377306, 0.731526, -0.567899), (-0.738433, -0.607723, -0.292217), (-0.558889, 0.3091, 0.76948)36.83431, 23.75626, -54.00787
44given(1), (1), (1)
45given(0.375829, -0.747124, 0.548232), (-0.743608, -0.596174, -0.302694), (0.552992, -0.293909, -0.779627)-36.33874, -25.95498, 54.38087
46given(-0.377049, 0.725509, -0.575736), (-0.73735, -0.611304, -0.28744), (-0.56049, 0.31614, 0.765445)37.54118, 23.3975, -53.7442

-
Components

-
PERIPLASMIC [NIFE] HYDROGENASE ... , 2 types, 6 molecules ABCQRS

#1: Protein PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT / NIFE HYDROGENLYASE SMALL CHAIN / NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28347.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: P18187, UniProt: E1K248*PLUS, cytochrome-c3 hydrogenase
#2: Protein PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT / NIFE HYDROGENLYASE LARGE CHAIN / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 59788.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) DESULFOVIBRIO FRUCTOSOVORANS JJ (bacteria)
References: UniProt: P18188, UniProt: E1K247*PLUS, cytochrome-c3 hydrogenase

-
Non-polymers , 7 types, 1733 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.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1701 / 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: 2.2 Å3/Da / Density % sol: 44.3 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3 / Details: INSIDE GLOVE ANAEROBIC BOX, PEG6000, MES, PH 6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.08→22 Å / Num. obs: 123504 / % possible obs: 87.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.1
Reflection shellResolution: 2.08→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.7 / % possible all: 57.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FRV

2frv


Resolution: 2.08→21.98 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.917 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES - WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23499 6255 5.1 %RANDOM
Rwork0.19475 ---
obs0.19677 117248 87.64 %-
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: 32.876 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å21.67 Å2
2---0.28 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.08→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18409 0 180 1701 20290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01919209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96726016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8152415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73724.45773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.958153055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611572
X-RAY DIFFRACTIONr_chiral_restr0.0880.22852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114386
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.029672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7182.29312083
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5711.0619537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
11A743tight positional0.040.05
12B743tight positional0.040.05
13C743tight positional0.040.05
11A359tight positional0.040.05
12B359tight positional0.050.05
13C359tight positional0.040.05
11A354tight positional0.090.05
12B354tight positional0.10.05
13C354tight positional0.110.05
11A148tight positional0.050.05
12B148tight positional0.040.05
13C148tight positional0.030.05
11A147tight positional0.040.05
12B147tight positional0.040.05
13C147tight positional0.030.05
11A10medium positional0.090.2
12B10medium positional0.070.2
13C10medium positional0.10.2
21A13medium positional0.240.2
22B13medium positional0.240.2
23C13medium positional0.470.2
31A10medium positional0.070.2
32B10medium positional0.050.2
33C10medium positional0.040.2
41A13medium positional0.030.2
42B13medium positional0.050.2
43C13medium positional0.030.2
51A17medium positional0.050.2
52B17medium positional0.030.2
53C17medium positional0.050.2
61A3medium positional0.030.2
62B3medium positional0.020.2
63C3medium positional0.020.2
71A16medium positional0.050.2
72B16medium positional0.060.2
73C16medium positional0.070.2
91Q22medium positional0.050.2
92R22medium positional0.040.2
93S22medium positional0.030.2
101Q57medium positional0.040.2
102R57medium positional0.050.2
103S57medium positional0.050.2
121Q38medium positional0.530.2
122R38medium positional0.290.2
123S38medium positional0.280.2
131Q17medium positional0.050.2
132R17medium positional0.040.2
133S17medium positional0.030.2
141Q35medium positional0.030.2
142R35medium positional0.030.2
143S35medium positional0.030.2
11A27loose positional0.25
12B27loose positional0.155
13C27loose positional0.255
21A29loose positional0.065
22B29loose positional0.055
23C29loose positional0.045
31A26loose positional0.145
32B26loose positional0.175
33C26loose positional0.15
41A44loose positional0.095
42B44loose positional0.095
43C44loose positional0.145
51A51loose positional0.055
52B51loose positional0.035
53C51loose positional0.045
61A32loose positional0.365
62B32loose positional0.155
63C32loose positional0.275
71A1loose positional0.075
72B1loose positional0.035
73C1loose positional0.055
81Q70loose positional0.095
82R70loose positional0.085
83S70loose positional0.125
91Q140loose positional0.085
92R140loose positional0.065
93S140loose positional0.085
101Q273loose positional0.125
102R273loose positional0.075
103S273loose positional0.075
121Q76loose positional0.265
122R76loose positional0.255
123S76loose positional0.435
131Q48loose positional0.075
132R48loose positional0.065
133S48loose positional0.045
141Q26loose positional0.065
142R26loose positional0.065
143S26loose positional0.095
11A350tight thermal3.731
12B350tight thermal1.081
13C350tight thermal3.441
21A197tight thermal4.171
22B197tight thermal1.421
23C197tight thermal4.411
31A360tight thermal4.441
32B360tight thermal2.931
33C360tight thermal2.21
41A44tight thermal4.111
42B44tight thermal1.91
43C44tight thermal2.541
51A177tight thermal4.521
52B177tight thermal5.521
53C177tight thermal1.941
61A163tight thermal3.411
62B163tight thermal4.471
63C163tight thermal1.261
71A263tight thermal3.671
72B263tight thermal3.381
73C263tight thermal1.11
81Q809tight thermal3.41
82R809tight thermal1.871
83S809tight thermal3.251
91Q377tight thermal3.721
92R377tight thermal2.141
93S377tight thermal5.691
101Q743tight thermal3.961
102R743tight thermal2.091
103S743tight thermal3.41
121Q354tight thermal4.31
122R354tight thermal1.521
123S354tight thermal4.371
131Q148tight thermal4.441
132R148tight thermal1.071
133S148tight thermal5.061
141Q147tight thermal4.611
142R147tight thermal1.251
143S147tight thermal5.051
11A10medium thermal2.992
12B10medium thermal1.832
13C10medium thermal4.782
21A13medium thermal4.292
22B13medium thermal2.292
23C13medium thermal6.012
31A10medium thermal4.482
32B10medium thermal1.532
33C10medium thermal2.982
41A13medium thermal4.012
42B13medium thermal2.282
43C13medium thermal1.842
51A17medium thermal4.782
52B17medium thermal6.552
53C17medium thermal1.852
61A3medium thermal3.912
62B3medium thermal5.052
63C3medium thermal1.142
71A16medium thermal3.222
72B16medium thermal1.712
73C16medium thermal2.162
91Q22medium thermal2.062
92R22medium thermal1.932
93S22medium thermal3.92
101Q57medium thermal4.282
102R57medium thermal2.072
103S57medium thermal5.732
121Q38medium thermal4.012
122R38medium thermal1.722
123S38medium thermal5.132
131Q17medium thermal4.62
132R17medium thermal1.012
133S17medium thermal5.582
141Q35medium thermal5.462
142R35medium thermal0.912
143S35medium thermal5.372
11A27loose thermal2.810
12B27loose thermal1.0710
13C27loose thermal2.9410
21A29loose thermal4.3510
22B29loose thermal1.1510
23C29loose thermal4.8310
31A26loose thermal4.5910
32B26loose thermal2.4410
33C26loose thermal3.2510
41A44loose thermal4.7510
42B44loose thermal2.1910
43C44loose thermal3.2210
51A51loose thermal4.910
52B51loose thermal6.9710
53C51loose thermal2.6710
61A32loose thermal3.8410
62B32loose thermal4.9310
63C32loose thermal1.2510
71A1loose thermal1.1110
72B1loose thermal2.0210
73C1loose thermal0.9110
81Q70loose thermal3.3810
82R70loose thermal2.2910
83S70loose thermal4.5810
91Q140loose thermal3.8110
92R140loose thermal2.5410
93S140loose thermal5.9810
101Q273loose thermal4.0110
102R273loose thermal2.6910
103S273loose thermal2.9210
121Q76loose thermal4.6110
122R76loose thermal1.4310
123S76loose thermal5.1310
131Q48loose thermal4.4510
132R48loose thermal1.1610
133S48loose thermal4.3810
141Q26loose thermal4.3210
142R26loose thermal2.5310
143S26loose thermal5.3310
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 336 -
Rwork0.233 5893 -
obs--60.3 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8111-0.049-0.33750.7361-0.05841.14010.00240.00280.08350.08750.0325-0.0507-0.12750.0372-0.03490.0384-0.0061-0.05020.03780.01070.1612.346314.78555.1264
20.48730.0465-0.04080.74340.10750.87230.0056-0.0365-0.05470.17190.0037-0.04360.16330.0394-0.00930.07130.0072-0.04720.04730.00650.15338.0942-6.801514.9962
30.8506-0.0959-0.07610.9587-0.10451.3928-0.0833-0.0991-0.21360.2462-0.0610.2590.2939-0.21310.14430.2329-0.03570.07990.22160.02750.2842-39.0545-46.479652.7081
40.6704-0.1152-0.18010.87080.32831.1145-0.0611-0.1414-0.00220.19850.0781-0.03850.05970.1511-0.01690.13740.0225-0.01850.19320.01070.1636-19.2318-33.102949.2412
51.0530.5451-0.75041.4163-0.39272.26320.1118-0.11270.02670.187-0.12430.2250.1417-0.24520.01250.2103-0.04510.02390.2081-0.0640.1822-16.89865.752761.7759
61.10080.3959-0.56961.2576-0.11061.90660.3212-0.43640.14070.3988-0.26990.0856-0.3190.1961-0.05130.4168-0.18230.06360.3155-0.09220.1522-5.076918.901278.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A265 - 267
3X-RAY DIFFRACTION2Q6 - 549
4X-RAY DIFFRACTION2Q550 - 553
5X-RAY DIFFRACTION3B3 - 264
6X-RAY DIFFRACTION3B265 - 267
7X-RAY DIFFRACTION4R5 - 549
8X-RAY DIFFRACTION4R550 - 553
9X-RAY DIFFRACTION5C5 - 264
10X-RAY DIFFRACTION5C265 - 267
11X-RAY DIFFRACTION6S6 - 549
12X-RAY DIFFRACTION6S550 - 553

+
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