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- PDB-4ud2: Structure of anaerobically purified D. fructosovorans NiFe- hydro... -

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Basic information

Entry
Database: PDB / ID: 4ud2
TitleStructure of anaerobically purified D. fructosovorans NiFe- hydrogenase
Components
  • HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
KeywordsOXIDOREDUCTASE / 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
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSIVORANS JJ (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 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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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)269,35038
Polymers264,4076
Non-polymers4,94332
Water17,691982
1
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09016
Polymers88,1362
Non-polymers1,95514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-125.3 kcal/mol
Surface area25510 Å2
MethodPISA
2
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,53810
Polymers88,1362
Non-polymers1,4028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-124.3 kcal/mol
Surface area25280 Å2
MethodPISA
3
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 area9560 Å2
ΔGint-122.8 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.010, 100.170, 183.980
Angle α, β, γ (deg.)90.00, 91.42, 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
15Q
25R
35S
16Q
26R
36S
17Q
27R
37S

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAA8 - 288 - 28
211SERSERILEILEBB8 - 288 - 28
311SERSERILEILECC8 - 288 - 28
121TYRTYRILEILEAA31 - 3631 - 36
221TYRTYRILEILEBB31 - 3631 - 36
321TYRTYRILEILECC31 - 3631 - 36
131ILEILEGLYGLYAA40 - 5340 - 53
231ILEILEGLYGLYBB40 - 5340 - 53
331ILEILEGLYGLYCC40 - 5340 - 53
141ALAALAGLUGLUAA56 - 5756 - 57
241ALAALAGLUGLUBB56 - 5756 - 57
341ALAALAGLUGLUCC56 - 5756 - 57
151ALAALALEULEUAA59 - 6059 - 60
251ALAALALEULEUBB59 - 6059 - 60
351ALAALALEULEUCC59 - 6059 - 60
161ALAALALEULEUAA63 - 6463 - 64
261ALAALALEULEUBB63 - 6463 - 64
361ALAALALEULEUCC63 - 6463 - 64
171GLYGLYTYRTYRAA69 - 7069 - 70
271GLYGLYTYRTYRBB69 - 7069 - 70
371GLYGLYTYRTYRCC69 - 7069 - 70
181LEULEUILEILEAA72 - 8172 - 81
281LEULEUILEILEBB72 - 8172 - 81
381LEULEUILEILECC72 - 8172 - 81
191TRPTRPGLYGLYAA86 - 9186 - 91
291TRPTRPGLYGLYBB86 - 9186 - 91
391TRPTRPGLYGLYCC86 - 9186 - 91
1101PROPROMETMETAA93 - 9493 - 94
2101PROPROMETMETBB93 - 9493 - 94
3101PROPROMETMETCC93 - 9493 - 94
112ALAALAALAALAAA101101
212ALAALAALAALABB101101
312ALAALAALAALACC101101
122GLYGLYALAALAAA107 - 130107 - 130
222GLYGLYALAALABB107 - 130107 - 130
322GLYGLYALAALACC107 - 130107 - 130
132GLYGLYVALVALAA132 - 133132 - 133
232GLYGLYVALVALBB132 - 133132 - 133
332GLYGLYVALVALCC132 - 133132 - 133
142THRTHRVALVALAA141 - 159141 - 159
242THRTHRVALVALBB141 - 159141 - 159
342THRTHRVALVALCC141 - 159141 - 159
152SF4SF4SF4SF4AM1267
252SF4SF4SF4SF4BP1267
352SF4SF4SF4SF4CS1267
113GLYGLYPROPROAA173 - 175173 - 175
213GLYGLYPROPROBB173 - 175173 - 175
313GLYGLYPROPROCC173 - 175173 - 175
123PHEPHETYRTYRAA178 - 179178 - 179
223PHEPHETYRTYRBB178 - 179178 - 179
323PHEPHETYRTYRCC178 - 179178 - 179
133VALVALCYSCYSAA183 - 187183 - 187
233VALVALCYSCYSBB183 - 187183 - 187
333VALVALCYSCYSCC183 - 187183 - 187
143ALAALAPHEPHEAA199 - 202199 - 202
243ALAALAPHEPHEBB199 - 202199 - 202
343ALAALAPHEPHECC199 - 202199 - 202
153SERSERSERSERAA204204
253SERSERSERSERBB204204
353SERSERSERSERCC204204
163ALAALALYSLYSAA207 - 208207 - 208
263ALAALALYSLYSBB207 - 208207 - 208
363ALAALALYSLYSCC207 - 208207 - 208
173GLYGLYLEULEUAA210 - 213210 - 213
273GLYGLYLEULEUBB210 - 213210 - 213
373GLYGLYLEULEUCC210 - 213210 - 213
183LEULEUGLYGLYAA216 - 220216 - 220
283LEULEUGLYGLYBB216 - 220216 - 220
383LEULEUGLYGLYCC216 - 220216 - 220
193VALVALPROPROAA222 - 228222 - 228
293VALVALPROPROBB222 - 228222 - 228
393VALVALPROPROCC222 - 228222 - 228
1103VALVALASNASNAA230 - 233230 - 233
2103VALVALASNASNBB230 - 233230 - 233
3103VALVALASNASNCC230 - 233230 - 233
114VALVALTRPTRPAA235 - 254235 - 254
214VALVALTRPTRPBB235 - 254235 - 254
314VALVALTRPTRPCC235 - 254235 - 254
124THRTHRTHRTHRAA256 - 258256 - 258
224THRTHRTHRTHRBB256 - 258256 - 258
324THRTHRTHRTHRCC256 - 258256 - 258
134PHEPHETYRTYRAA260 - 261260 - 261
234PHEPHETYRTYRBB260 - 261260 - 261
334PHEPHETYRTYRCC260 - 261260 - 261
144SF4SF4F3SF3SAK - L1265 - 1266
244SF4SF4F3SF3SBN - O1265 - 1266
344SF4SF4F3SF3SCQ - R1265 - 1266
115PROPROVALVALQD15 - 3215 - 32
215PROPROVALVALRE15 - 3215 - 32
315PROPROVALVALSF15 - 3215 - 32
125ASPASPLEULEUQD41 - 5641 - 56
225ASPASPLEULEURE41 - 5641 - 56
325ASPASPLEULEUSF41 - 5641 - 56
135GLYGLYPROPROQD58 - 6158 - 61
235GLYGLYPROPRORE58 - 6158 - 61
335GLYGLYPROPROSF58 - 6158 - 61
145GLYGLYVALVALQD58 - 9158 - 91
245GLYGLYVALVALRE58 - 9158 - 91
345GLYGLYVALVALSF58 - 9158 - 91
155ILEILEHISHISQD95 - 11595 - 115
255ILEILEHISHISRE95 - 11595 - 115
355ILEILEHISHISSF95 - 11595 - 115
165VALVALVALVALQD117 - 130117 - 130
265VALVALVALVALRE117 - 130117 - 130
365VALVALVALVALSF117 - 130117 - 130
175GLYGLYTHRTHRQD177 - 180177 - 180
275GLYGLYTHRTHRRE177 - 180177 - 180
375GLYGLYTHRTHRSF177 - 180177 - 180
185VALVALTYRTYRQD197 - 205197 - 205
285VALVALTYRTYRRE197 - 205197 - 205
385VALVALTYRTYRSF197 - 205197 - 205
195ALAALATYRTYRQD215 - 240215 - 240
295ALAALATYRTYRRE215 - 240215 - 240
395ALAALATYRTYRSF215 - 240215 - 240
1105GLYGLYMETMETQD423 - 439423 - 439
2105GLYGLYMETMETRE423 - 439423 - 439
3105GLYGLYMETMETSF423 - 439423 - 439
116GLYGLYILEILEQD468 - 483468 - 483
216GLYGLYILEILERE468 - 483468 - 483
316GLYGLYILEILESF468 - 483468 - 483
126PHEPHEPROPROQD493 - 505493 - 505
226PHEPHEPROPRORE493 - 505493 - 505
326PHEPHEPROPROSF493 - 505493 - 505
136GLYGLYALAALAQD521 - 525521 - 525
236GLYGLYALAALARE521 - 525521 - 525
336GLYGLYALAALASF521 - 525521 - 525
146PROPROILEILEQD530 - 533530 - 533
246PROPROILEILERE530 - 533530 - 533
346PROPROILEILESF530 - 533530 - 533
156LEULEUHISHISQD534 - 549534 - 549
256LEULEUHISHISRE534 - 549534 - 549
356LEULEUHISHISSF534 - 549534 - 549
166FCOFCOMGMGQX - Z1550 - 1553
266FCOFCOMGMGREA - GA1550 - 1553
366FCOFCOMGMGSJA - LA1550 - 1553
117TRPTRPTHRTHRQD280 - 286280 - 286
217TRPTRPTHRTHRRE280 - 286280 - 286
317TRPTRPTHRTHRSF280 - 286280 - 286
127TYRTYRASPASPQD289 - 299289 - 299
227TYRTYRASPASPRE289 - 299289 - 299
327TYRTYRASPASPSF289 - 299289 - 299
137SERSERPROPROQD301 - 302301 - 302
237SERSERPROPRORE301 - 302301 - 302
337SERSERPROPROSF301 - 302301 - 302
147LYSLYSGLYGLYQD304 - 318304 - 318
247LYSLYSGLYGLYRE304 - 318304 - 318
347LYSLYSGLYGLYSF304 - 318304 - 318
157TYRTYRTYRTYRQD368 - 376368 - 376
257TYRTYRTYRTYRRE368 - 376368 - 376
357TYRTYRTYRTYRSF368 - 376368 - 376
167ALAALAALAALAQD380 - 392380 - 392
267ALAALAALAALARE380 - 392380 - 392
367ALAALAALAALASF380 - 392380 - 392

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(0.394084, -0.742879, 0.541136), (-0.752696, -0.598735, -0.273799), (0.527397, -0.299411, -0.795113)29.479, 73.222, 54.915
2given(0.382932, 0.736109, 0.558128), (0.730626, -0.611054, 0.304629), (0.565286, 0.291131, -0.771812)-6.078, 54.241, 114.513
3given(0.393052, -0.74116, 0.544235), (-0.748576, -0.601633, -0.278697), (0.533988, -0.297858, -0.791288)29.438, 73.299, 54.815
4given(0.377663, 0.737822, 0.559455), (0.729662, -0.609117, 0.310756), (0.570056, 0.290852, -0.768402)-6.025, 54.192, 114.482
5given(1), (1), (1)
6given(0.393184, -0.751641, 0.529567), (-0.74346, -0.598777, -0.297882), (0.540993, -0.276589, -0.794245)14.39451, 82.14066, 47.9015
7given(0.380482, 0.729708, 0.56812), (0.736053, -0.610867, 0.291664), (0.559875, 0.307193, -0.769527)-102.26631, 4.20119, 74.85831
8given(1), (1), (1)
9given(0.394611, -0.751177, 0.529164), (-0.742338, -0.60002, -0.29818), (0.541495, -0.275153, -0.794402)14.37379, 82.19463, 47.80804
10given(0.380988, 0.729748, 0.567728), (0.736154, -0.610933, 0.291268), (0.559397, 0.306966, -0.769966)-102.19445, 4.26064, 74.92897
11given(1), (1), (1)
12given(0.397995, -0.753297, 0.523587), (-0.741408, -0.600249, -0.300026), (0.540291, -0.268783, -0.797397)14.7234, 82.24326, 47.63004
13given(0.384113, 0.732823, 0.561629), (0.737837, -0.60931, 0.290412), (0.555027, 0.30284, -0.774747)-101.65601, 4.24022, 75.76542
14given(1), (1), (1)
15given(0.397865, -0.753191, 0.523838), (-0.740151, -0.600896, -0.301829), (0.542107, -0.267632, -0.796551)14.70173, 82.3811, 47.47059
16given(0.383549, 0.731481, 0.563761), (0.738005, -0.60975, 0.289057), (0.555193, 0.305191, -0.773705)-101.85749, 4.45149, 75.47581
17given(1), (1), (1)
18given(0.393592, -0.748665, 0.533466), (-0.74068, -0.601983, -0.298346), (0.544498, -0.277701, -0.791457)14.03122, 82.26584, 47.71397
19given(0.377886, 0.729371, 0.570281), (0.737426, -0.609549, 0.290952), (0.559826, 0.310593, -0.768197)-102.53432, 4.17587, 74.47753
20given(1), (1), (1)
21given(0.394552, -0.747103, 0.534945), (-0.740075, -0.603435, -0.296909), (0.544626, -0.278753, -0.790999)13.81174, 82.28048, 47.77606
22given(0.377038, 0.729849, 0.570231), (0.737399, -0.609079, 0.292002), (0.560433, 0.310392, -0.767835)-102.55385, 4.02521, 74.47393
23given(1), (1), (1)
24given(0.393746, -0.748166, 0.534052), (-0.741102, -0.602089, -0.297079), (0.543812, -0.278814, -0.791538)13.98691, 82.22865, 47.83534
25given(0.378354, 0.728972, 0.570481), (0.736692, -0.610292, 0.291255), (0.560477, 0.310071, -0.767934)-102.5083, 4.1846, 74.50328

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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 / Fragment: RESIDUES 51-314 / Source method: isolated from a natural source
Source: (natural) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K248, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 59788.328 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-549 / Source method: isolated from a natural source
Source: (natural) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K247, cytochrome-c3 hydrogenase

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Non-polymers , 7 types, 1014 molecules

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


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


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#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.: 982 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4
Details: VAPOR DIFFUSION, PH 6.4, 293 K, PEG6000, MES, IN A GLOVEBOX

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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: Apr 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 92983 / % possible obs: 88.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.7 / % possible all: 52.9

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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→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.145 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.589 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20688 4628 5 %RANDOM
Rwork0.17308 ---
obs0.17475 88317 88.65 %-
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: 37.384 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å20 Å21.83 Å2
2---2.12 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18396 0 180 982 19558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01919148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.96525935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.06452414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18424.407767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.696153023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0131572
X-RAY DIFFRACTIONr_chiral_restr0.0840.22842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114346
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_it2.5812.6469665
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5644.9512073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3882.7489483
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 / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4906.08
12B4902.59
13C4906.5
21A3217.2
22B3213.59
23C3214.82
31A2827.32
32B2828.7
33C2823.25
41A2176.85
42B2176.67
43C2172.22
51Q12525.33
52R12524.34
53S12527.3
61Q4135.78
62R4134.99
63S4139.35
71Q4337.75
72R4333.65
73S4339.54
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 234 -
Rwork0.228 3776 -
obs--52.82 %
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)
10.0294-0.0163-0.09760.2932-0.08420.44580.00010.00530.0220.06230.0173-0.0404-0.02020.0328-0.01740.01450.00520.00510.08370.00490.158712.503214.74455.1089
20.0656-0.0409-0.04130.35340.06730.2971-0.0420.0316-0.01950.11060.02040.01660.07890.00080.02160.05690.00360.02510.05870.0040.11678.2084-6.84515.0006
30.2486-0.0755-0.13640.22520.29660.4094-0.088-0.0016-0.08780.1511-0.070.13840.1993-0.1140.1580.1107-0.03440.11580.10950.01050.172726.220753.615553.0326
40.2373-0.061-0.15520.23270.25360.6316-0.0357-0.0553-0.00290.05320.02430.06440.0110.10450.01140.03470.02650.0450.11170.01840.109545.907467.075149.3554
50.3657-0.3225-0.28590.70870.21160.97690.03290.0184-0.00530.0358-0.1059-0.03110.11760.11190.0730.06760.01740.02320.10220.01610.081612.199955.8836122.0399
60.4112-0.3508-0.29360.7240.03590.81790.19150.16520.0292-0.103-0.223-0.0615-0.111-0.14330.03150.11360.07130.02390.15080.01320.02410.431769.0749105.6992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A1265 - 1267
3X-RAY DIFFRACTION2Q6 - 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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