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- PDB-4ue6: Structure of methylene blue-treated anaerobically purified D. fru... -

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Basic information

Entry
Database: PDB / ID: 4ue6
TitleStructure of methylene blue-treated anaerobically purified D. fructosovorans NiFe-hydrogenase
Components
  • HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
KeywordsOXIDOREDUCTASE / NI-SIB STATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / 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 FRUCTOSOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,89033
Polymers264,4076
Non-polymers4,48327
Water18,8801048
1
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,72212
Polymers88,1362
Non-polymers1,58610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-121.6 kcal/mol
Surface area25280 Å2
MethodPISA
2
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
S: NICKEL-DEPENDENT 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 area8800 Å2
ΔGint-122.3 kcal/mol
Surface area25120 Å2
MethodPISA
3
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,72212
Polymers88,1362
Non-polymers1,58610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-121.9 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.280, 99.550, 184.020
Angle α, β, γ (deg.)90.00, 91.16, 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
17Q
27R
37S
18Q
28R
38S
19Q
29R
39S
110Q
210R
310S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A7
2113B7
3113C7
1211A8 - 27
2211B8 - 27
3211C8 - 27
1313A28
2313B28
3313C28
1413A30
2413B30
3413C30
1511A31 - 36
2511B31 - 36
3511C31 - 36
1613A37 - 39
2613B37 - 39
3613C37 - 39
1711A40 - 53
2711B40 - 53
3711C40 - 53
1813A54
2813B54
3813C54
1911A55 - 57
2911B55 - 57
3911C55 - 57
11011A59 - 60
21011B59 - 60
31011C59 - 60
1121A63 - 64
2121B63 - 64
3121C63 - 64
1223A65 - 66
2223B65 - 66
3223C65 - 66
1323A68
2323B68
3323C68
1421A69 - 70
2421B69 - 70
3421C69 - 70
1523A71
2523B71
3523C71
1621A72 - 81
2621B72 - 81
3621C72 - 81
1723A83 - 85
2723B83 - 85
3723C83 - 85
1821A86 - 91
2821B86 - 91
3821C86 - 91
1923A92
2923B92
3923C92
11021A93 - 94
21021B93 - 94
31021C93 - 94
1133A95 - 98
2133B95 - 98
3133C95 - 98
1231A101 - 102
2231B101 - 102
3231C101 - 102
1333A103
2333B103
3333C103
1433A105 - 107
2433B105 - 107
3433C105 - 107
1531A108 - 133
2531B108 - 133
3531C108 - 133
1633A138
2633B138
3633C138
1731A141 - 159
2731B141 - 159
3731C141 - 159
1833A160 - 166
2833B160 - 166
3833C160 - 166
1931A267
2931B267
3931C267
1143A167 - 170
2143B167 - 170
3143C167 - 170
1241A173 - 176
2241B173 - 176
3241C173 - 176
1343A177
2343B177
3343C177
1441A178 - 179
2441B178 - 179
3441C178 - 179
1543A180 - 181
2543B180 - 181
3543C180 - 181
1641A183 - 187
2641B183 - 187
3641C183 - 187
1743A188 - 191
2743B188 - 191
3743C188 - 191
1843A193
2843B193
3843C193
1943A195
2943B195
3943C195
11043A197 - 198
21043B197 - 198
31043C197 - 198
1151A199 - 202
2151B199 - 202
3151C199 - 202
1253A203
2253B203
3253C203
1351A204
2351B204
3351C204
1453A206
2453B206
3453C206
1551A207 - 208
2551B207 - 208
3551C207 - 208
1653A209
2653B209
3653C209
1751A210 - 213
2751B210 - 213
3751C210 - 213
1853A214
2853B214
3853C214
1951A216 - 223
2951B216 - 223
3951C216 - 223
11053A224
21053B224
31053C224
1161A225 - 228
2161B225 - 228
3161C225 - 228
1261A230 - 233
2261B230 - 233
3261C230 - 233
1363A234
2363B234
3363C234
1461A235 - 257
2461B235 - 257
3461C235 - 257
1563A258 - 259
2563B258 - 259
3563C258 - 259
1661A260 - 261
2661B260 - 261
3661C260 - 261
1761A265 - 266
2761B265 - 266
3761C265 - 266
1173Q6 - 14
2173R6 - 14
3173S6 - 14
1271Q15 - 32
2271R15 - 32
3271S15 - 32
1373Q33 - 40
2373R33 - 40
3373S33 - 40
1471Q41 - 56
2471R41 - 56
3471S41 - 56
1571Q58 - 91
2571R58 - 91
3571S58 - 91
1673Q93 - 94
2673R93 - 94
3673S93 - 94
1771Q95 - 115
2771R95 - 115
3771S95 - 115
1871Q117 - 121
2871R117 - 121
3871S117 - 121
1971Q123 - 130
2971R123 - 130
3971S123 - 130
11071Q132 - 133
21071R132 - 133
31071S132 - 133
1181Q41 - 142
2181R41 - 142
3181S41 - 142
1283Q151 - 159
2283R151 - 159
3283S151 - 159
1383Q161 - 176
2383R161 - 176
3383S161 - 176
1481Q177 - 180
2481R177 - 180
3481S177 - 180
1583Q181 - 188
2583R181 - 188
3583S181 - 188
1683Q190 - 194
2683R190 - 194
3683S190 - 194
1781Q195 - 205
2781R195 - 205
3781S195 - 205
1883Q206 - 214
2883R206 - 214
3883S206 - 214
1981Q215 - 240
2981R215 - 240
3981S215 - 240
11083Q241 - 279
21083R241 - 279
31083S241 - 279
1191Q280 - 286
2191R280 - 286
3191S280 - 286
1291Q289 - 299
2291R289 - 299
3291S289 - 299
1391Q301 - 318
2391R301 - 318
3391S301 - 318
1493Q319 - 341
2493R319 - 341
3493S319 - 341
1593Q345 - 358
2593R345 - 358
3593S345 - 358
1691Q368 - 376
2691R368 - 376
3691S368 - 376
1791Q380 - 392
2791R380 - 392
3791S380 - 392
1893Q393 - 402
2893R393 - 402
3893S393 - 402
1993Q406 - 422
2993R406 - 422
3993S406 - 422
11091Q423 - 439
21091R423 - 439
31091S423 - 439
11103Q440 - 463
21103R440 - 463
31103S440 - 463
12103Q465 - 467
22103R465 - 467
32103S465 - 467
13101Q468 - 483
23101R468 - 483
33101S468 - 483
14103Q484 - 492
24103R484 - 492
34103S484 - 492
15101Q493 - 508
25101R493 - 508
35101S493 - 508
16103Q510 - 520
26103R510 - 520
36103S510 - 520
17101Q521 - 525
27101R521 - 525
37101S521 - 525
18103Q529 - 531
28103R529 - 531
38103S529 - 531
19101Q534 - 549
29101R534 - 549
39101S534 - 549
110101Q550 - 553
210101R550 - 553
310101S550 - 553

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.386253, -0.75618, 0.528204), (-0.748516, -0.591593, -0.29957), (0.539011, -0.279659, -0.794517)14.7911, 82.12025, 47.6438
3given(0.383348, 0.738933, 0.554096), (0.742602, -0.603307, 0.290796), (0.549169, 0.299997, -0.78001)-101.0623, 3.3203, 76.65022
4given(1), (1), (1)
5given(0.387597, -0.756769, 0.526374), (-0.750025, -0.59087, -0.297213), (0.53594, -0.279595, -0.796615)14.8398, 81.9673, 47.7961
6given(0.384451, 0.738113, 0.554424), (0.741608, -0.604595, 0.290658), (0.549741, 0.299422, -0.779828)-101.08881, 3.37642, 76.6612
7given(1), (1), (1)
8given(0.391841, -0.75521, 0.525471), (-0.749158, -0.593443, -0.294257), (0.534063, -0.278359, -0.798307)14.73045, 81.94951, 47.85855
9given(0.385143, 0.739728, 0.551785), (0.741847, -0.603813, 0.291672), (0.548933, 0.297004, -0.78132)-100.85298, 3.21511, 76.96193
10given(1), (1), (1)
11given(0.396579, -0.758499, 0.517111), (-0.746475, -0.594318, -0.299266), (0.534322, -0.267328, -0.801895)15.26921, 82.09875, 47.48555
12given(0.389865, 0.744908, 0.541403), (0.745704, -0.600333, 0.289007), (0.540306, 0.291052, -0.78953)-99.88671, 3.26358, 78.43426
13given(1), (1), (1)
14given(0.396504, -0.756169, 0.52057), (-0.741207, -0.59826, -0.304462), (0.541661, -0.26513, -0.79769)15.01963, 82.53719, 46.93573
15given(0.386145, 0.74406, 0.545221), (0.748265, -0.598314, 0.286567), (0.539436, 0.297314, -0.78779)-100.27481, 3.48692, 77.81779
16given(1), (1), (1)
17given(0.390438, -0.755162, 0.526582), (-0.741932, -0.596744, -0.305668), (0.545063, -0.271343, -0.793271)14.71746, 82.54634, 46.90356
18given(0.384773, 0.7416, 0.549526), (0.746459, -0.600202, 0.287326), (0.542908, 0.299644, -0.784516)-100.69889, 3.50438, 77.23779
19given(1), (1), (1)
20given(0.386635, -0.752056, 0.533784), (-0.744759, -0.595981, -0.300235), (0.543919, -0.281459, -0.790527)14.26851, 82.30283, 47.41609
21given(0.381279, 0.739968, 0.554143), (0.74453, -0.601112, 0.290413), (0.547998, 0.301847, -0.780119)-101.13988, 3.20354, 76.54575
22given(1), (1), (1)
23given(0.386631, -0.752285, 0.533464), (-0.744804, -0.595827, -0.300429), (0.54386, -0.281171, -0.79067)14.30446, 82.30746, 47.41046
24given(0.381688, 0.739604, 0.554347), (0.744618, -0.601372, 0.289648), (0.547594, 0.302221, -0.780259)-101.13984, 3.31264, 76.53809
25given(1), (1), (1)
26given(0.384196, -0.751549, 0.536253), (-0.746001, -0.594906, -0.299281), (0.543945, -0.285063, -0.789217)14.20842, 82.25901, 47.60435
27given(0.382658, 0.738264, 0.555463), (0.742986, -0.603249, 0.289934), (0.54913, 0.301756, -0.779358)-101.12726, 3.40369, 76.48495
28given(1), (1), (1)
29given(0.386292, -0.752297, 0.533692), (-0.745006, -0.595617, -0.300344), (0.543825, -0.281583, -0.790548)14.29526, 82.29076, 47.42966
30given(0.382669, 0.738818, 0.554719), (0.743367, -0.602754, 0.289988), (0.548607, 0.301391, -0.779868)-101.12193, 3.35878, 76.55493
31given(0.388163, -0.746939, 0.539825), (-0.756138, -0.59299, -0.276799), (0.526863, -0.300739, -0.794966)30.009, 73.048, 54.657
32given(0.384604, 0.744155, 0.546181), (0.740444, -0.602026, 0.298844), (0.551202, 0.289479, -0.782546)-5.766, 53.688, 114.902
33given(0.385762, -0.744971, 0.544248), (-0.752055, -0.595617, -0.282229), (0.534416, -0.300431, -0.790026)30, 73.137, 54.568
34given(0.381373, 0.744326, 0.548209), (0.739317, -0.601592, 0.302486), (0.554946, 0.28994, -0.779724)-5.788, 53.661, 114.826

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Components

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Protein , 2 types, 6 molecules ABCQRS

#1: Protein HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28347.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / / NIFE-HYDROGENASE LARGE SUBUNIT


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

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Non-polymers , 7 types, 1075 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.: 9 / 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.: 1048 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.2
Details: CRYSTAL GROWN IN GLOVE BOX, PEG6000, MES, PH 6.2, SOAKED 2 HOURS IN A METHYLENE BLUE SOLUTION BEFORE FLASH-FREEZING AND DATA COLLECTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→23.9 Å / Num. obs: 99290 / % possible obs: 94.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.3 / % possible all: 76.5

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Processing

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

2frv


Resolution: 2.3→23.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.289 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES - WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18141 4970 5 %RANDOM
Rwork0.15066 ---
obs0.15219 94319 94.88 %-
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: 32.856 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å21.41 Å2
2---0.79 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18403 0 150 1048 19601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01919102
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.96525889
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86652411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41424.399766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.323153021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4911572
X-RAY DIFFRACTIONr_chiral_restr0.0840.22835
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114338
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_it1.0242.1359662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6093.59912067
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6682.3149440
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
11A590tight positional0.020.03
12B590tight positional0.020.03
13C590tight positional0.020.03
11A26loose positional0.027
12B26loose positional0.027
13C26loose positional0.027
21A28loose positional0.027
22B28loose positional0.027
23C28loose positional0.027
31A47loose positional0.027
32B47loose positional0.027
33C47loose positional0.027
41A61loose positional0.027
42B61loose positional0.027
43C61loose positional0.027
51A30loose positional0.027
52B30loose positional0.037
53C30loose positional0.027
61A11loose positional0.037
62B11loose positional0.037
63C11loose positional0.037
71Q64loose positional0.067
72R64loose positional0.067
73S64loose positional0.127
81Q323loose positional0.027
82R323loose positional0.027
83S323loose positional0.027
91Q243loose positional0.047
92R243loose positional0.047
93S243loose positional0.057
101Q195loose positional0.097
102R195loose positional0.127
103S195loose positional0.067
11A360tight thermal1.421.5
12B360tight thermal1.541.5
13C360tight thermal1.561.5
21A187tight thermal1.251.5
22B187tight thermal1.131.5
23C187tight thermal1.261.5
31A387tight thermal1.311.5
32B387tight thermal1.481.5
33C387tight thermal1.541.5
41A153tight thermal2.081.5
42B153tight thermal2.251.5
43C153tight thermal1.361.5
51A150tight thermal1.321.5
52B150tight thermal1.981.5
53C150tight thermal1.491.5
61A278tight thermal1.291.5
62B278tight thermal1.251.5
63C278tight thermal1.071.5
71Q902tight thermal1.141.5
72R902tight thermal1.271.5
73S902tight thermal1.381.5
81Q1441tight thermal1.441.5
82R1441tight thermal1.451.5
83S1441tight thermal1.821.5
91Q813tight thermal1.621.5
92R813tight thermal1.471.5
93S813tight thermal1.881.5
101Q590tight thermal1.171.5
102R590tight thermal1.341.5
103S590tight thermal1.451.5
11A26loose thermal1.8415
12B26loose thermal2.0415
13C26loose thermal2.5715
21A28loose thermal6.1715
22B28loose thermal2.1115
23C28loose thermal5.2515
31A47loose thermal3.515
32B47loose thermal3.3615
33C47loose thermal2.6115
41A61loose thermal2.3115
42B61loose thermal2.4415
43C61loose thermal1.7115
51A30loose thermal315
52B30loose thermal4.0415
53C30loose thermal1.9615
61A11loose thermal2.315
62B11loose thermal1.4615
63C11loose thermal1.1415
71Q64loose thermal2.7415
72R64loose thermal2.7915
73S64loose thermal4.4515
81Q323loose thermal2.7715
82R323loose thermal2.615
83S323loose thermal3.0315
91Q243loose thermal2.615
92R243loose thermal2.3815
93S243loose thermal2.9215
101Q195loose thermal2.3215
102R195loose thermal2.6315
103S195loose thermal2.915
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 292 -
Rwork0.235 5118 -
obs--70.68 %
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)
11.2321-0.2066-0.66160.6276-0.05731.2765-0.0043-0.03850.12230.05790.0283-0.0041-0.14960.0008-0.0240.08540.003-0.06310.00580.010.11612.596514.82155.0701
20.5460.0017-0.02650.61330.00530.8564-0.0209-0.0551-0.03860.04010.0171-0.03370.1230.02220.00380.09720.0048-0.04850.02860.01460.13228.0925-6.615714.997
31.0583-0.07340.02151.0431-0.20131.7388-0.0476-0.0648-0.15860.0939-0.03560.20590.3757-0.23250.08320.1537-0.04540.02160.10470.02610.222726.555353.307852.7763
40.6521-0.0763-0.06630.78140.11241.0031-0.0301-0.1073-0.03140.07020.0213-0.05540.1310.16330.00880.07160.03-0.05140.10950.02210.14446.235166.765349.0748
50.6838-0.1826-0.3961.32670.57912.25730.07510.07-0.0504-0.0074-0.0608-0.16220.06770.2138-0.01430.05630.0128-0.07010.08150.03230.13212.742555.5683122.2336
60.7574-0.075-0.24910.79850.11191.47620.17290.27010.1405-0.1018-0.1041-0.0486-0.2804-0.121-0.06890.1590.1023-0.02170.1980.05420.16230.583768.1908105.7498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A1265 - 1267
3X-RAY DIFFRACTION2Q5 - 549
4X-RAY DIFFRACTION2Q1550 - 1553
5X-RAY DIFFRACTION3B3 - 264
6X-RAY DIFFRACTION3B1265 - 1267
7X-RAY DIFFRACTION4R6 - 549
8X-RAY DIFFRACTION4R1550 - 1553
9X-RAY DIFFRACTION5C5 - 264
10X-RAY DIFFRACTION5C1265 - 1267
11X-RAY DIFFRACTION6S6 - 549
12X-RAY DIFFRACTION6S1550 - 1553

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