[English] 日本語
Yorodumi
- PDB-6g94: Structure of E. coli hydrogenase-1 C19G variant in complex with c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g94
TitleStructure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b
Components
  • (Hydrogenase-1 ...) x 2
  • Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit
KeywordsOXIDOREDUCTASE / new [4Fe-4S] cluster
Function / homology
Function and homology information


hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity ...hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / respiratory electron transport chain / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Nickel-dependent hydrogenase b-type cytochrome subunit / Nickel-dependent hydrogenases b-type cytochrome subunit signature 1. / Nickel-dependent hydrogenases b-type cytochrome subunit signature 2. / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit ...Nickel-dependent hydrogenase b-type cytochrome subunit / Nickel-dependent hydrogenases b-type cytochrome subunit signature 1. / Nickel-dependent hydrogenases b-type cytochrome subunit signature 2. / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / 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 / Di-haem cytochrome, transmembrane / 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 / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fe4S4 / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / IRON/SULFUR CLUSTER / Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit / Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit / Hydrogenase-1 large chain / Hydrogenase-1 small chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Citation
Journal: Chem. Commun. (Camb.) / Year: 2018
Title: X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster.
Authors: Volbeda, A. / Mouesca, J.M. / Darnault, C. / Roessler, M.M. / Parkin, A. / Armstrong, F.A. / Fontecilla-Camps, J.C.
#1: Journal: Structure / Year: 2013
Title: Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b.
Authors: Volbeda, A. / Darnault, C. / Parkin, A. / Sargent, F. / Armstrong, F.A. / Fontecilla-Camps, J.C.
#2: Journal: J. Am. Chem. Soc. / Year: 2013
Title: Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases.
Authors: Evans, R.M. / Parkin, A. / Roessler, M.M. / Murphy, B.J. / Adamson, H. / Lukey, M.J. / Sargent, F. / Volbeda, A. / Fontecilla-Camps, J.C. / Armstrong, F.A.
#3: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2012
Title: X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Authors: Volbeda, A. / Amara, P. / Darnault, C. / Mouesca, J.M. / Parkin, A. / Roessler, M.M. / Armstrong, F.A. / Fontecilla-Camps, J.C.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 5, 2020Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
Q: Hydrogenase-1 small chain
J: Hydrogenase-1 large chain
R: Hydrogenase-1 small chain
K: Hydrogenase-1 large chain
A: Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit
B: Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,57940
Polymers461,33210
Non-polymers6,24730
Water12,647702
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.410, 165.030, 206.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
31Q
41R
12S
22T
32Q
42R
13S
23T
33Q
43R
14S
24Q
15S
25Q
16L
26M
36J
46K
17L
27M
37J
47K
18L
28M
38J
48K
19L
29M
39J
49K
110T
210R
111T
211R
112A
212B
113E
213F
313G
413H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111S6 - 15
2111T6 - 15
3111Q6 - 15
4111R6 - 15
1211S17 - 36
2211T17 - 36
3211Q17 - 36
4211R17 - 36
1311S40 - 57
2311T40 - 57
3311Q40 - 57
4311R40 - 57
1411S59 - 60
2411T59 - 60
3411Q59 - 60
4411R59 - 60
1511S62 - 65
2511T62 - 65
3511Q62 - 65
4511R62 - 65
1611S67 - 93
2611T67 - 93
3611Q67 - 93
4611R67 - 93
1711S95 - 102
2711T95 - 102
3711Q95 - 102
4711R95 - 102
1811S104 - 106
2811T104 - 106
3811Q104 - 106
4811R104 - 106
1911S112 - 124
2911T112 - 124
3911Q112 - 124
4911R112 - 124
11011S343 - 350
21011T343 - 350
31011Q343 - 350
41011R343 - 350
1121S126 - 135
2121T126 - 135
3121Q126 - 135
4121R126 - 135
1221S137 - 138
2221T137 - 138
3221Q137 - 138
4221R137 - 138
1321S140 - 167
2321T140 - 167
3321Q140 - 167
4321R140 - 167
1421S169 - 172
2421T169 - 172
3421Q169 - 172
4421R169 - 172
1131S176 - 184
2131T176 - 184
3131Q176 - 184
4131R176 - 184
1231S186 - 187
2231T186 - 187
3231Q186 - 187
4231R186 - 187
1331S189 - 192
2331T189 - 192
3331Q189 - 192
4331R189 - 192
1431S194 - 196
2431T194 - 196
3431Q194 - 196
4431R194 - 196
1531S198 - 216
2531T198 - 216
3531Q198 - 216
4531R198 - 216
1631S219 - 255
2631T219 - 255
3631Q219 - 255
4631R219 - 255
1731S257 - 259
2731T257 - 259
3731Q257 - 259
4731R257 - 259
1142S261 - 265
2142Q261 - 265
1152S278 - 286
2152Q278 - 286
1161L7 - 10
2161M7 - 10
3161J7 - 10
4161K7 - 10
1261L12 - 15
2261M12 - 15
3261J12 - 15
4261K12 - 15
1361L19 - 38
2361M19 - 38
3361J19 - 38
4361K19 - 38
1461L41 - 60
2461M41 - 60
3461J41 - 60
4461K41 - 60
1561L64 - 138
2561M64 - 138
3561J64 - 138
4561K64 - 138
1661L145 - 146
2661M145 - 146
3661J145 - 146
4661K145 - 146
1761L148 - 149
2761M148 - 149
3761J148 - 149
4761K148 - 149
1861L151 - 153
2861M151 - 153
3861J151 - 153
4861K151 - 153
1961L155 - 168
2961M155 - 168
3961J155 - 168
4961K155 - 168
11061L173 - 174
21061M173 - 174
31061J173 - 174
41061K173 - 174
1171L176 - 182
2171M176 - 182
3171J176 - 182
4171K176 - 182
1271L185 - 244
2271M185 - 244
3271J185 - 244
4271K185 - 244
1371L247 - 255
2371M247 - 255
3371J247 - 255
4371K247 - 255
1471L257 - 268
2471M257 - 268
3471J257 - 268
4471K257 - 268
1571L270 - 279
2571M270 - 279
3571J270 - 279
4571K270 - 279
1671L281 - 283
2671M281 - 283
3671J281 - 283
4671K281 - 283
1771L288 - 290
2771M288 - 290
3771J288 - 290
4771K288 - 290
1871L292 - 315
2871M292 - 315
3871J292 - 315
4871K292 - 315
1971L318 - 331
2971M318 - 331
3971J318 - 331
4971K318 - 331
11071L334 - 342
21071M334 - 342
31071J334 - 342
41071K334 - 342
1181L344 - 354
2181M344 - 354
3181J344 - 354
4181K344 - 354
1281L356 - 371
2281M356 - 371
3281J356 - 371
4281K356 - 371
1381L395 - 428
2381M395 - 428
3381J395 - 428
4381K395 - 428
1481L443 - 471
2481M443 - 471
3481J443 - 471
4481K443 - 471
1581L473 - 486
2581M473 - 486
3581J473 - 486
4581K473 - 486
1681L490 - 497
2681M490 - 497
3681J490 - 497
4681K490 - 497
1781L499
2781M499
3781J499
4781K499
1881L501 - 518
2881M501 - 518
3881J501 - 518
4881K501 - 518
1191L521 - 522
2191M521 - 522
3191J521 - 522
4191K521 - 522
1291L526 - 541
2291M526 - 541
3291J526 - 541
4291K526 - 541
1391L543 - 558
2391M543 - 558
3391J543 - 558
4391K543 - 558
1491L563 - 590
2491M563 - 590
3491J563 - 590
4491K563 - 590
11102T261 - 272
21102R261 - 272
12102T274 - 275
22102R274 - 275
11112T278 - 283
21112R278 - 283
12112T285 - 286
22112R285 - 286
13112T288
23112R288
14112T290 - 293
24112R290 - 293
11121A23 - 73
21121B23 - 73
12121A131 - 132
22121B131 - 132
13121A134 - 151
23121B134 - 151
14121A159 - 163
24121B159 - 163
15121A165 - 187
25121B165 - 187
16121A189 - 195
26121B189 - 195
17121A301 - 317
27121B301 - 317
11131E1 - 49
21131F1 - 49
31131G1 - 49
41131H1 - 49
12131E51 - 56
22131F51 - 56
32131G51 - 56
42131H51 - 56
13131E58 - 88
23131F58 - 88
33131G58 - 88
43131H58 - 88
14131E90 - 120
24131F90 - 120
34131G90 - 120
44131H90 - 120
15131E122 - 161
25131F122 - 161
35131G122 - 161
45131H122 - 161
16131E163 - 164
26131F163 - 164
36131G163 - 164
46131H163 - 164
17131E167 - 171
27131F167 - 171
37131G167 - 171
47131H167 - 171

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.970771, 0.03411, -0.237571), (0.042785, -0.949401, -0.31114), (-0.236163, -0.31221, 0.920191)-37.929211, 13.40058, -2.48158
3given(-0.661269, 0.002711, 0.750144), (0.006076, -0.999941, 0.00897), (0.750125, 0.01049, 0.661213)37.219139, 10.25319, -16.81736
4given(0.46722, -0.038955, -0.883283), (-0.268795, 0.945483, -0.18388), (0.842291, 0.323334, 0.431278)-69.729843, 10.53673, -29.80826
5given(1), (1), (1)
6given(-0.970417, 0.032, -0.239304), (0.044519, -0.950464, -0.30763), (-0.237294, -0.309183, 0.920922)-37.979099, 13.58366, -2.51463
7given(-0.662567, 0.004344, 0.74899), (0.005723, -0.999925, 0.010862), (0.748981, 0.011483, 0.662492)37.24781, 10.2859, -16.75021
8given(0.463731, -0.038301, -0.885148), (-0.266431, 0.946792, -0.180553), (0.844966, 0.319559, 0.428852)-69.72364, 10.63286, -29.99988
9given(1), (1), (1)
10given(-0.969517, 0.038297, -0.242014), (0.039248, -0.950684, -0.307669), (-0.241862, -0.307788, 0.920201)-38.012341, 13.4207, -2.65974
11given(-0.664418, 0.00385, 0.747351), (0.006083, -0.999926, 0.010559), (0.747336, 0.011562, 0.664346)37.213032, 10.30006, -16.630489
12given(0.464551, -0.043644, -0.88447), (-0.262389, 0.94715, -0.184552), (0.84578, 0.317809, 0.428548)-69.667, 10.26564, -30.05929
13given(1), (1), (1)
14given(-0.68753, 0.005137, 0.726138), (0.006834, -0.999885, 0.013544), (0.726124, 0.014274, 0.687416)36.54364, 10.41147, -14.98331
15given(1), (1), (1)
16given(-0.691494, -0.003064, 0.722376), (0.010238, -0.999932, 0.005559), (0.72231, 0.011239, 0.691478)36.00779, 9.93381, -14.70131
17given(1), (1), (1)
18given(-0.971193, 0.033234, -0.235967), (0.043357, -0.949055, -0.312115), (-0.234318, -0.313354, 0.920274)-37.893398, 13.33099, -2.46327
19given(-0.660269, 0.000507, 0.751029), (0.009078, -0.999921, 0.008656), (0.750974, 0.012533, 0.660213)37.20414, 10.13498, -16.918039
20given(0.469595, -0.034389, -0.882212), (-0.270266, 0.945672, -0.180724), (0.840498, 0.323299, 0.434788)-69.873703, 10.67083, -29.61018
21given(1), (1), (1)
22given(-0.971122, 0.034825, -0.23603), (0.042138, -0.948703, -0.313348), (-0.234835, -0.314245, 0.919838)-37.88398, 13.29166, -2.49758
23given(-0.66189, 0.002236, 0.749598), (0.00819, -0.999914, 0.010215), (0.749556, 0.012901, 0.661815)37.24445, 10.21703, -16.80514
24given(0.468879, -0.036942, -0.88249), (-0.270096, 0.945268, -0.183075), (0.840952, 0.324197, 0.433239)-69.817886, 10.56085, -29.72534
25given(1), (1), (1)
26given(-0.971088, 0.032368, -0.236519), (0.044931, -0.948276, -0.31425), (-0.234457, -0.315791, 0.919405)-37.946602, 13.33624, -2.55277
27given(-0.662517, -0.000349, 0.749046), (0.0096, -0.999922, 0.008026), (0.748985, 0.012508, 0.662469)37.168812, 10.09418, -16.76333
28given(0.467532, -0.033096, -0.883357), (-0.272235, 0.945339, -0.179503), (0.841013, 0.324404, 0.432966)-69.933907, 10.80165, -29.736139
29given(1), (1), (1)
30given(-0.971268, 0.031071, -0.235951), (0.045669, -0.948681, -0.312919), (-0.233565, -0.314704, 0.920005)-37.971931, 13.39108, -2.47105
31given(-0.660069, -0.003946, 0.751195), (0.012104, -0.999912, 0.005383), (0.751108, 0.012645, 0.660058)37.02187, 9.95238, -16.922489
32given(0.469431, -0.030042, -0.882458), (-0.272197, 0.945823, -0.176997), (0.839966, 0.32329, 0.435821)-70.053719, 10.9478, -29.528311
33given(1), (1), (1)
34given(-0.656074, 0.012424, 0.754594), (-0.019205, -0.999816, -0.000235), (0.754452, -0.014646, 0.656192)37.32196, 10.00363, -16.7069
35given(1), (1), (1)
36given(-0.685688, 0.033296, 0.727133), (-0.021969, -0.999445, 0.025048), (0.727564, 0.001201, 0.686039)35.405788, 11.50258, -14.73069
37given(1), (1), (1)
38given(-0.668455, -0.000138, 0.743753), (0.014214, -0.99982, 0.01259), (0.743617, 0.018988, 0.668336)37.039799, 10.34618, -16.35074
39given(1), (1), (1)
40given(-0.970946, 0.034352, -0.236819), (0.04274, -0.948835, -0.312866), (-0.235449, -0.313898, 0.9198)-37.884239, 13.31695, -2.50124
41given(-0.662227, 0.001049, 0.749303), (0.008591, -0.999923, 0.008992), (0.749254, 0.012392, 0.662167)37.23011, 10.17634, -16.782221
42given(0.467727, -0.036806, -0.883106), (-0.269977, 0.945434, -0.182393), (0.841632, 0.323728, 0.432268)-69.776901, 10.60632, -29.770411

-
Components

-
Hydrogenase-1 ... , 2 types, 8 molecules STQRLMJK

#1: Protein
Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 36768.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C19G variant / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli)
References: UniProt: P69739, UniProt: P69740*PLUS, hydrogenase (acceptor)
#2: Protein
Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64751.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACD8, hydrogenase (acceptor)

-
Protein , 1 types, 2 molecules AB

#3: Protein Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit


Mass: 27626.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hyaC, b0974, JW0956 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAM1, UniProt: P0AAM2*PLUS

-
Non-polymers , 9 types, 732 molecules

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


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


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#6: Chemical
ChemComp-ER2 / Fe4S4 / Cubane-type cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3FeN2O
#8: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: PEG4000, NaAc, NH4Ac, DTT, DMM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97908 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.5→49.67 Å / Num. obs: 146009 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.305 / Rpim(I) all: 0.161 / Rrim(I) all: 0.347 / Net I/σ(I): 6.5 / Num. measured all: 656127
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.594.62.194141920.2791.1472.48499.1
9.68-49.674.10.03727250.9980.020.04298.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GD3

4gd3


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 37.343 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.827 / ESU R Free: 0.307 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 7064 4.9 %RANDOM
Rwork0.2219 ---
obs0.2234 136263 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.44 Å2 / Biso mean: 52.019 Å2 / Biso min: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29537 0 218 702 30457
Biso mean--45.92 41.12 -
Num. residues----3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01930675
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.94741735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96653822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65923.7521338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.582154632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.815173
X-RAY DIFFRACTIONr_chiral_restr0.0740.24502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02123604
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11S56TIGHT POSITIONAL0.070.05
11S52TIGHT POSITIONAL0.060.05
11S911TIGHT POSITIONAL0.070.05
11S163TIGHT POSITIONAL0.040.05
12T163TIGHT POSITIONAL0.040.05
13Q163TIGHT POSITIONAL0.050.05
14R163TIGHT POSITIONAL0.050.05
11S781TIGHT THERMAL4.414
12T781TIGHT THERMAL3.724
13Q781TIGHT THERMAL3.24
14R781TIGHT THERMAL4.064
21S330TIGHT THERMAL4.974
22T330TIGHT THERMAL3.574
23Q330TIGHT THERMAL3.14
24R330TIGHT THERMAL4.754
31S603TIGHT THERMAL3.414
32T603TIGHT THERMAL2.924
33Q603TIGHT THERMAL3.114
34R603TIGHT THERMAL2.854
41S19MEDIUM POSITIONAL0.080.5
41S20TIGHT THERMAL2.264
41S19MEDIUM THERMAL2.158
51S22MEDIUM POSITIONAL0.070.5
51S36TIGHT THERMAL2.594
51S22MEDIUM THERMAL4.028
61L1139TIGHT THERMAL3.574
62M1139TIGHT THERMAL3.474
63J1139TIGHT THERMAL2.74
64K1139TIGHT THERMAL3.034
71L1132TIGHT THERMAL3.244
72M1132TIGHT THERMAL3.044
73J1132TIGHT THERMAL3.354
74K1132TIGHT THERMAL3.14
81L1031TIGHT THERMAL3.174
82M1031TIGHT THERMAL3.54
83J1031TIGHT THERMAL3.424
84K1031TIGHT THERMAL3.244
91L425TIGHT THERMAL3.794
92M425TIGHT THERMAL3.554
93J425TIGHT THERMAL3.044
94K425TIGHT THERMAL2.854
101T51MEDIUM POSITIONAL0.10.5
101T56TIGHT THERMAL2.684
101T51MEDIUM THERMAL3.28
111T24MEDIUM POSITIONAL0.110.5
111T52TIGHT THERMAL1.914
111T24MEDIUM THERMAL1.88
121Q911TIGHT THERMAL3.014
131Q163TIGHT THERMAL2.194
132S163TIGHT THERMAL2.254
133T163TIGHT THERMAL2.464
134R163TIGHT THERMAL2.374
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 439 -
Rwork0.378 8577 -
all-9016 -
obs--84.43 %
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)
10.9040.2423-0.0671.069-0.2741.06990.0191-0.0381-0.03020.12750.0546-0.0666-0.00950.1684-0.07370.55720.0363-0.00330.1773-0.02550.02465.78924.519-11.584
21.0395-0.12910.80260.6916-0.21071.4660.0160.0926-0.0232-0.04680.01830.0555-0.056-0.0225-0.03430.5420.00850.00330.1493-0.0190.0617-11.86822.208-32.5
30.10230.05230.13830.73840.13260.6548-0.0117-0.05240.00330.0284-0.01230.0359-0.114-0.08680.02410.57740.03460.01910.14330.00670.0323-14.8335.057-3.633
40.70950.4648-0.22741.45790.18470.92380.0465-0.02830.0368-0.00240.01510.21270.0982-0.2686-0.06160.545-0.0454-0.03960.25860.01940.1441-39.503-6.287-22.517
50.92060.562-0.78070.8217-0.10330.9569-0.06250.06760.0045-0.02990.02520.05650.0333-0.08870.03730.5457-0.014-0.00480.1564-0.00090.1-17.8451.868-36.465
60.27270.2141-0.07870.6490.0880.63790.035-0.0488-0.02080.0717-0.01260.00550.2099-0.0751-0.02250.6419-0.0467-0.01840.11820.02250.0559-21.118-19.48-13.297
70.5055-0.05120.20970.65870.21760.71760.0019-0.1038-0.08550.1875-0.0080.03640.00970.02540.00610.66590.0074-0.01110.1396-0.02460.037224.742-14.433-20.057
80.89830.00680.19841.23750.01551.03110.01840.0155-0.0147-0.17010.00250.14590.01080.0808-0.02090.604-0.00560.01370.1328-0.05340.040920.81-12.265-47.079
90.327-0.10010.18140.4814-0.14750.51260.04920.0459-0.06060.0119-0.0329-0.08140.09670.1445-0.01630.62610.0536-0.01280.1627-0.0740.072944.638-24.663-30.043
100.91240.35040.14731.0581-0.35430.7962-0.04770.1974-0.1144-0.19840.068-0.08850.00450.2123-0.02030.6616-0.02230.09240.2834-0.01690.027446.61716.318-61.459
111.52260.3121-0.49260.52880.12710.90230.03570.07950.0111-0.1066-0.00910.0855-0.010.0546-0.02670.6122-0.00360.02950.1572-0.02950.028221.7047.979-54.402
120.36410.14570.10020.6865-0.1760.2975-0.01120.05090.0035-0.0017-0.0422-0.0492-0.07310.11570.05340.6331-0.03130.02190.18040.01240.012441.08229.516-41.603
131.14020.46030.21731.0184-0.00220.7702-0.0170.1724-0.0086-0.25-0.00380.16740.0592-0.12370.02080.67720.0129-0.02310.25050.00850.0928-23.9043.646-61.589
140.51450.6991-0.45261.4136-0.21161.5606-0.05470.17670.0814-0.18240.09120.2374-0.02920.054-0.03660.67810.0045-0.04480.2538-0.02990.08188.9154.945-75.445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S3 - 172
2X-RAY DIFFRACTION1S343
3X-RAY DIFFRACTION2S173 - 266
4X-RAY DIFFRACTION2S341 - 342
5X-RAY DIFFRACTION3L2 - 582
6X-RAY DIFFRACTION3L583 - 590
7X-RAY DIFFRACTION4T4 - 172
8X-RAY DIFFRACTION4T343
9X-RAY DIFFRACTION5T173 - 266
10X-RAY DIFFRACTION5T341 - 342
11X-RAY DIFFRACTION6M2 - 582
12X-RAY DIFFRACTION6M583 - 590
13X-RAY DIFFRACTION7Q4 - 172
14X-RAY DIFFRACTION7Q343
15X-RAY DIFFRACTION8Q173 - 266
16X-RAY DIFFRACTION8Q341 - 342
17X-RAY DIFFRACTION9J2 - 582
18X-RAY DIFFRACTION9J583 - 590
19X-RAY DIFFRACTION10R4 - 172
20X-RAY DIFFRACTION10R343
21X-RAY DIFFRACTION11R173 - 266
22X-RAY DIFFRACTION11R341 - 342
23X-RAY DIFFRACTION12K2 - 582
24X-RAY DIFFRACTION12K583 - 590
25X-RAY DIFFRACTION13S267 - 297
26X-RAY DIFFRACTION13T267 - 299
27X-RAY DIFFRACTION13A14 - 89
28X-RAY DIFFRACTION13A100 - 113
29X-RAY DIFFRACTION13A126 - 207
30X-RAY DIFFRACTION13A301
31X-RAY DIFFRACTION14Q267 - 298
32X-RAY DIFFRACTION14R267 - 294
33X-RAY DIFFRACTION14B14 - 83
34X-RAY DIFFRACTION14B101 - 114
35X-RAY DIFFRACTION14B127 - 202
36X-RAY DIFFRACTION14B301

+
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