PDB-4ueq: Structure of the V74C large subunit mutant of D. fructosovorans N...

ID or keywords:

Entry

Database: PDB / ID: 4ueq

Title

Structure of the V74C large subunit mutant of D. fructosovorans NiFe- hydrogenase

Components

HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

Keywords

OXIDOREDUCTASE / NIFE-HYDROGENASE MUTANT / NICKEL-CARBOXAMIDO BOND / OXYGEN- TOLERANCE

Function / homology

Function and homology information

cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...
Similarity search - Function

Biological species

DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Volbeda, A. / Martin, L. / Liebgott, P.-P. / Fontecilla-Camps, J.C.

Citation

Journal: 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

Deposition	Dec 18, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 2.0	Jan 23, 2019	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_struct_conn_angle 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 / _pdbx_struct_conn_angle.value
Revision 2.1	Dec 20, 2023	Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 2.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ueq.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb4ueq.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	4ueq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ueq_validation.pdf.gz	544.4 KB	Display	wwPDB validaton report
Full document	4ueq_full_validation.pdf.gz	561.7 KB	Display
Data in XML	4ueq_validation.xml.gz	88 KB	Display
Data in CIF	4ueq_validation.cif.gz	159.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ue/4ueq ftp://data.pdbj.org/pub/pdb/validation_reports/ue/4ueq	HTTPS FTP

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Related structure data

Related structure data	4ud2C 4ud6C 4ue2C 4ue6C 4uewC 1yqwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1e3d-1 4ud6-2 4ud6-1 1yrq-6 4urh-3 1ubr-d 1yrq-4 3cus-3 3cus-1 4urh-1 1yrq-1 1yqw-1 3h3x-3 4uqp-2 4uew-3 4u9h-d 7ll3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (19) #144 - Dec 2011 Complex I similarity (3) #220 - Apr 2018 Dehalogenases similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1) #193 - Jan 2016 Siderocalin similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#111 - Mar 2009
Hydrogenase
similarity (19)
#144 - Dec 2011
Complex I
similarity (3)
#220 - Apr 2018
Dehalogenases
similarity (2)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#193 - Jan 2016
Siderocalin
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#35 - Nov 2002
Ferritin and Transferrin
similarity (1)
#37 - Jan 2003
Serum Albumin
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

D: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

E: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

F: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

T: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

U: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

V: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

546 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

T: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

V: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

E: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

U: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

hetero molecules

defined by author&software
91.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.720, 99.800, 190.800
Angle α, β, γ (deg.)	90.21, 98.61, 90.11
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	6 - 13
2	1	1	2	B	6 - 13
3	1	1	2	C	6 - 13
4	1	1	2	D	6 - 13
5	1	1	2	E	6 - 13
6	1	1	2	F	6 - 13
1	2	1	1	A	14 - 23
2	2	1	1	B	14 - 23
3	2	1	1	C	14 - 23
4	2	1	1	D	14 - 23
5	2	1	1	E	14 - 23
6	2	1	1	F	14 - 23
1	3	1	2	A	24 - 28
2	3	1	2	B	24 - 28
3	3	1	2	C	24 - 28
4	3	1	2	D	24 - 28
5	3	1	2	E	24 - 28
6	3	1	2	F	24 - 28
1	4	1	2	A	30 - 53
2	4	1	2	B	30 - 53
3	4	1	2	C	30 - 53
4	4	1	2	D	30 - 53
5	4	1	2	E	30 - 53
6	4	1	2	F	30 - 53
1	5	1	2	A	55 - 57
2	5	1	2	B	55 - 57
3	5	1	2	C	55 - 57
4	5	1	2	D	55 - 57
5	5	1	2	E	55 - 57
6	5	1	2	F	55 - 57
1	6	1	2	A	72 - 81
2	6	1	2	B	72 - 81
3	6	1	2	C	72 - 81
4	6	1	2	D	72 - 81
5	6	1	2	E	72 - 81
6	6	1	2	F	72 - 81
1	7	1	2	A	83 - 87
2	7	1	2	B	83 - 87
3	7	1	2	C	83 - 87
4	7	1	2	D	83 - 87
5	7	1	2	E	83 - 87
6	7	1	2	F	83 - 87
1	8	1	2	A	89 - 95
2	8	1	2	B	89 - 95
3	8	1	2	C	89 - 95
4	8	1	2	D	89 - 95
5	8	1	2	E	89 - 95
6	8	1	2	F	89 - 95
1	9	1	2	A	105 - 110
2	9	1	2	B	105 - 110
3	9	1	2	C	105 - 110
4	9	1	2	D	105 - 110
5	9	1	2	E	105 - 110
6	9	1	2	F	105 - 110
1	10	1	1	A	267
2	10	1	1	B	267
3	10	1	1	C	267
4	10	1	1	D	267
5	10	1	1	E	267
6	10	1	1	F	267
1	1	2	1	A	111 - 117
2	1	2	1	B	111 - 117
3	1	2	1	C	111 - 117
4	1	2	1	D	111 - 117
5	1	2	1	E	111 - 117
6	1	2	1	F	111 - 117
1	2	2	1	A	145 - 151
2	2	2	1	B	145 - 151
3	2	2	1	C	145 - 151
4	2	2	1	D	145 - 151
5	2	2	1	E	145 - 151
6	2	2	1	F	145 - 151
1	3	2	2	A	118 - 123
2	3	2	2	B	118 - 123
3	3	2	2	C	118 - 123
4	3	2	2	D	118 - 123
5	3	2	2	E	118 - 123
6	3	2	2	F	118 - 123
1	4	2	2	A	125 - 130
2	4	2	2	B	125 - 130
3	4	2	2	C	125 - 130
4	4	2	2	D	125 - 130
5	4	2	2	E	125 - 130
6	4	2	2	F	125 - 130
1	5	2	2	A	141 - 144
2	5	2	2	B	141 - 144
3	5	2	2	C	141 - 144
4	5	2	2	D	141 - 144
5	5	2	2	E	141 - 144
6	5	2	2	F	141 - 144
1	6	2	2	A	152 - 158
2	6	2	2	B	152 - 158
3	6	2	2	C	152 - 158
4	6	2	2	D	152 - 158
5	6	2	2	E	152 - 158
6	6	2	2	F	152 - 158
1	7	2	2	A	172 - 175
2	7	2	2	B	172 - 175
3	7	2	2	C	172 - 175
4	7	2	2	D	172 - 175
5	7	2	2	E	172 - 175
6	7	2	2	F	172 - 175
1	1	3	2	A	178 - 180
2	1	3	2	B	178 - 180
3	1	3	2	C	178 - 180
4	1	3	2	D	178 - 180
5	1	3	2	E	178 - 180
6	1	3	2	F	178 - 180
1	2	3	1	A	182 - 190
2	2	3	1	B	182 - 190
3	2	3	1	C	182 - 190
4	2	3	1	D	182 - 190
5	2	3	1	E	182 - 190
6	2	3	1	F	182 - 190
1	3	3	2	A	191 - 193
2	3	3	2	B	191 - 193
3	3	3	2	C	191 - 193
4	3	3	2	D	191 - 193
5	3	3	2	E	191 - 193
6	3	3	2	F	191 - 193
1	4	3	2	A	195 - 207
2	4	3	2	B	195 - 207
3	4	3	2	C	195 - 207
4	4	3	2	D	195 - 207
5	4	3	2	E	195 - 207
6	4	3	2	F	195 - 207
1	5	3	1	A	210 - 213
2	5	3	1	B	210 - 213
3	5	3	1	C	210 - 213
4	5	3	1	D	210 - 213
5	5	3	1	E	210 - 213
6	5	3	1	F	210 - 213
1	6	3	1	A	216 - 228
2	6	3	1	B	216 - 228
3	6	3	1	C	216 - 228
4	6	3	1	D	216 - 228
5	6	3	1	E	216 - 228
6	6	3	1	F	216 - 228
1	7	3	2	A	230 - 241
2	7	3	2	B	230 - 241
3	7	3	2	C	230 - 241
4	7	3	2	D	230 - 241
5	7	3	2	E	230 - 241
6	7	3	2	F	230 - 241
1	8	3	1	A	242 - 251
2	8	3	1	B	242 - 251
3	8	3	1	C	242 - 251
4	8	3	1	D	242 - 251
5	8	3	1	E	242 - 251
6	8	3	1	F	242 - 251
1	9	3	2	A	252 - 258
2	9	3	2	B	252 - 258
3	9	3	2	C	252 - 258
4	9	3	2	D	252 - 258
5	9	3	2	E	252 - 258
6	9	3	2	F	252 - 258
1	10	3	1	A	265 - 266
2	10	3	1	B	265 - 266
3	10	3	1	C	265 - 266
4	10	3	1	D	265 - 266
5	10	3	1	E	265 - 266
6	10	3	1	F	265 - 266
1	1	4	1	Q	68 - 79
2	1	4	1	R	68 - 79
3	1	4	1	S	68 - 79
4	1	4	1	T	68 - 79
5	1	4	1	U	68 - 79
6	1	4	1	V	68 - 79
1	2	4	1	Q	539 - 549
2	2	4	1	R	539 - 549
3	2	4	1	S	539 - 549
4	2	4	1	T	539 - 549
5	2	4	1	U	539 - 549
6	2	4	1	V	539 - 549
1	3	4	1	Q	550 - 555
2	3	4	1	R	550 - 555
3	3	4	1	S	550 - 555
4	3	4	1	T	550 - 555
5	3	4	1	U	550 - 555
6	3	4	1	V	550 - 555
1	1	5	2	Q	7 - 34
2	1	5	2	R	7 - 34
3	1	5	2	S	7 - 34
4	1	5	2	T	7 - 34
5	1	5	2	U	7 - 34
6	1	5	2	V	7 - 34
1	2	5	2	Q	37 - 39
2	2	5	2	R	37 - 39
3	2	5	2	S	37 - 39
4	2	5	2	T	37 - 39
5	2	5	2	U	37 - 39
6	2	5	2	V	37 - 39
1	3	5	2	Q	41 - 56
2	3	5	2	R	41 - 56
3	3	5	2	S	41 - 56
4	3	5	2	T	41 - 56
5	3	5	2	U	41 - 56
6	3	5	2	V	41 - 56
1	4	5	2	Q	59 - 67
2	4	5	2	R	59 - 67
3	4	5	2	S	59 - 67
4	4	5	2	T	59 - 67
5	4	5	2	U	59 - 67
6	4	5	2	V	59 - 67
1	5	5	2	Q	80 - 91
2	5	5	2	R	80 - 91
3	5	5	2	S	80 - 91
4	5	5	2	T	80 - 91
5	5	5	2	U	80 - 91
6	5	5	2	V	80 - 91
1	6	5	2	Q	93 - 100
2	6	5	2	R	93 - 100
3	6	5	2	S	93 - 100
4	6	5	2	T	93 - 100
5	6	5	2	U	93 - 100
6	6	5	2	V	93 - 100
1	7	5	2	Q	102 - 124
2	7	5	2	R	102 - 124
3	7	5	2	S	102 - 124
4	7	5	2	T	102 - 124
5	7	5	2	U	102 - 124
6	7	5	2	V	102 - 124
1	8	5	2	Q	126 - 134
2	8	5	2	R	126 - 134
3	8	5	2	S	126 - 134
4	8	5	2	T	126 - 134
5	8	5	2	U	126 - 134
6	8	5	2	V	126 - 134
1	9	5	2	Q	146 - 153
2	9	5	2	R	146 - 153
3	9	5	2	S	146 - 153
4	9	5	2	T	146 - 153
5	9	5	2	U	146 - 153
6	9	5	2	V	146 - 153
1	10	5	2	Q	155 - 157
2	10	5	2	R	155 - 157
3	10	5	2	S	155 - 157
4	10	5	2	T	155 - 157
5	10	5	2	U	155 - 157
6	10	5	2	V	155 - 157
1	1	6	2	Q	162 - 165
2	1	6	2	R	162 - 165
3	1	6	2	S	162 - 165
4	1	6	2	T	162 - 165
5	1	6	2	U	162 - 165
6	1	6	2	V	162 - 165
1	2	6	2	Q	159 - 171
2	2	6	2	R	159 - 171
3	2	6	2	S	159 - 171
4	2	6	2	T	159 - 171
5	2	6	2	U	159 - 171
6	2	6	2	V	159 - 171
1	3	6	2	Q	173 - 175
2	3	6	2	R	173 - 175
3	3	6	2	S	173 - 175
4	3	6	2	T	173 - 175
5	3	6	2	U	173 - 175
6	3	6	2	V	173 - 175
1	4	6	2	Q	177 - 188
2	4	6	2	R	177 - 188
3	4	6	2	S	177 - 188
4	4	6	2	T	177 - 188
5	4	6	2	U	177 - 188
6	4	6	2	V	177 - 188
1	5	6	2	Q	190 - 194
2	5	6	2	R	190 - 194
3	5	6	2	S	190 - 194
4	5	6	2	T	190 - 194
5	5	6	2	U	190 - 194
6	5	6	2	V	190 - 194
1	6	6	2	Q	196 - 213
2	6	6	2	R	196 - 213
3	6	6	2	S	196 - 213
4	6	6	2	T	196 - 213
5	6	6	2	U	196 - 213
6	6	6	2	V	196 - 213
1	7	6	2	Q	215 - 240
2	7	6	2	R	215 - 240
3	7	6	2	S	215 - 240
4	7	6	2	T	215 - 240
5	7	6	2	U	215 - 240
6	7	6	2	V	215 - 240
1	1	7	2	Q	242 - 244
2	1	7	2	R	242 - 244
3	1	7	2	S	242 - 244
4	1	7	2	T	242 - 244
5	1	7	2	U	242 - 244
6	1	7	2	V	242 - 244
1	2	7	2	Q	247 - 249
2	2	7	2	R	247 - 249
3	2	7	2	S	247 - 249
4	2	7	2	T	247 - 249
5	2	7	2	U	247 - 249
6	2	7	2	V	247 - 249
1	3	7	2	Q	251 - 255
2	3	7	2	R	251 - 255
3	3	7	2	S	251 - 255
4	3	7	2	T	251 - 255
5	3	7	2	U	251 - 255
6	3	7	2	V	251 - 255
1	4	7	2	Q	261 - 277
2	4	7	2	R	261 - 277
3	4	7	2	S	261 - 277
4	4	7	2	T	261 - 277
5	4	7	2	U	261 - 277
6	4	7	2	V	261 - 277
1	5	7	2	Q	279 - 302
2	5	7	2	R	279 - 302
3	5	7	2	S	279 - 302
4	5	7	2	T	279 - 302
5	5	7	2	U	279 - 302
6	5	7	2	V	279 - 302
1	6	7	2	Q	305 - 322
2	6	7	2	R	305 - 322
3	6	7	2	S	305 - 322
4	6	7	2	T	305 - 322
5	6	7	2	U	305 - 322
6	6	7	2	V	305 - 322
1	1	8	2	Q	324 - 327
2	1	8	2	R	324 - 327
3	1	8	2	S	324 - 327
4	1	8	2	T	324 - 327
5	1	8	2	U	324 - 327
6	1	8	2	V	324 - 327
1	2	8	2	Q	332 - 336
2	2	8	2	R	332 - 336
3	2	8	2	S	332 - 336
4	2	8	2	T	332 - 336
5	2	8	2	U	332 - 336
6	2	8	2	V	332 - 336
1	3	8	2	Q	338 - 342
2	3	8	2	R	338 - 342
3	3	8	2	S	338 - 342
4	3	8	2	T	338 - 342
5	3	8	2	U	338 - 342
6	3	8	2	V	338 - 342
1	4	8	2	Q	345 - 347
2	4	8	2	R	345 - 347
3	4	8	2	S	345 - 347
4	4	8	2	T	345 - 347
5	4	8	2	U	345 - 347
6	4	8	2	V	345 - 347
1	5	8	2	Q	349 - 353
2	5	8	2	R	349 - 353
3	5	8	2	S	349 - 353
4	5	8	2	T	349 - 353
5	5	8	2	U	349 - 353
6	5	8	2	V	349 - 353
1	6	8	2	Q	355 - 357
2	6	8	2	R	355 - 357
3	6	8	2	S	355 - 357
4	6	8	2	T	355 - 357
5	6	8	2	U	355 - 357
6	6	8	2	V	355 - 357
1	7	8	2	Q	366 - 376
2	7	8	2	R	366 - 376
3	7	8	2	S	366 - 376
4	7	8	2	T	366 - 376
5	7	8	2	U	366 - 376
6	7	8	2	V	366 - 376
1	8	8	2	Q	380 - 394
2	8	8	2	R	380 - 394
3	8	8	2	S	380 - 394
4	8	8	2	T	380 - 394
5	8	8	2	U	380 - 394
6	8	8	2	V	380 - 394
1	9	8	2	Q	396 - 400
2	9	8	2	R	396 - 400
3	9	8	2	S	396 - 400
4	9	8	2	T	396 - 400
5	9	8	2	U	396 - 400
6	9	8	2	V	396 - 400
1	10	8	2	Q	403 - 409
2	10	8	2	R	403 - 409
3	10	8	2	S	403 - 409
4	10	8	2	T	403 - 409
5	10	8	2	U	403 - 409
6	10	8	2	V	403 - 409
1	1	9	2	Q	413 - 421
2	1	9	2	R	413 - 421
3	1	9	2	S	413 - 421
4	1	9	2	T	413 - 421
5	1	9	2	U	413 - 421
6	1	9	2	V	413 - 421
1	2	9	2	Q	423 - 439
2	2	9	2	R	423 - 439
3	2	9	2	S	423 - 439
4	2	9	2	T	423 - 439
5	2	9	2	U	423 - 439
6	2	9	2	V	423 - 439
1	3	9	2	Q	441 - 443
2	3	9	2	R	441 - 443
3	3	9	2	S	441 - 443
4	3	9	2	T	441 - 443
5	3	9	2	U	441 - 443
6	3	9	2	V	441 - 443
1	4	9	2	Q	445 - 447
2	4	9	2	R	445 - 447
3	4	9	2	S	445 - 447
4	4	9	2	T	445 - 447
5	4	9	2	U	445 - 447
6	4	9	2	V	445 - 447
1	5	9	2	Q	454 - 458
2	5	9	2	R	454 - 458
3	5	9	2	S	454 - 458
4	5	9	2	T	454 - 458
5	5	9	2	U	454 - 458
6	5	9	2	V	454 - 458
1	6	9	2	Q	468 - 485
2	6	9	2	R	468 - 485
3	6	9	2	S	468 - 485
4	6	9	2	T	468 - 485
5	6	9	2	U	468 - 485
6	6	9	2	V	468 - 485
1	7	9	2	Q	489 - 508
2	7	9	2	R	489 - 508
3	7	9	2	S	489 - 508
4	7	9	2	T	489 - 508
5	7	9	2	U	489 - 508
6	7	9	2	V	489 - 508
1	8	9	2	Q	513 - 516
2	8	9	2	R	513 - 516
3	8	9	2	S	513 - 516
4	8	9	2	T	513 - 516
5	8	9	2	U	513 - 516
6	8	9	2	V	513 - 516
1	9	9	2	Q	518 - 527
2	9	9	2	R	518 - 527
3	9	9	2	S	518 - 527
4	9	9	2	T	518 - 527
5	9	9	2	U	518 - 527
6	9	9	2	V	518 - 527
1	10	9	2	Q	529 - 538
2	10	9	2	R	529 - 538
3	10	9	2	S	529 - 538
4	10	9	2	T	529 - 538
5	10	9	2	U	529 - 538
6	10	9	2	V	529 - 538

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.549729, -0.790362, -0.27042), (-0.79159, -0.596279, 0.133556), (-0.266804, 0.140642, -0.953434)	23.959, 25.178, 60.182
2	given	(-0.558541, -0.773831, 0.298694), (0.772777, -0.616303, -0.151615), (0.30141, 0.146141, 0.942229)	-15.54, -5.49, 67.67
3	given	(-0.999996, -0.001296, 0.002319), (-0.00128, 0.999977, 0.006712), (-0.002327, 0.006709, -0.999975)	0.259, 49.887, -0.254
4	given	(-0.549203, 0.791558, 0.267978), (-0.794538, -0.59397, 0.126126), (0.259007, -0.14365, 0.955133)	-23.536, -24.289, -60.549
5	given	(0.55859, 0.77453, -0.296784), (0.775231, -0.614752, -0.145248), (-0.294947, -0.148942, -0.943834)	15.885, 44.853, -67.895
6	given	(0.548352, -0.791879, -0.268772), (-0.793822, -0.593986, 0.130489), (-0.262978, 0.141804, -0.954324)	23.906, 25.161, 60.197
7	given	(-0.560203, -0.771067, 0.3027), (0.770213, -0.61935, -0.152244), (0.304867, 0.147856, 0.940848)	-15.576, -5.599, 67.763
8	given	(-0.999995, -0.003128), (-0.003128, 0.999995), (-1)	0.227, 49.882, -0.226
9	given	(-0.54782, 0.793068, 0.266338), (-0.796405, -0.591858, 0.124268), (0.256187, -0.144037, 0.955835)	-23.492, -24.346, -60.528
10	given	(0.560086, 0.771792, -0.301065), (0.772825, -0.617669, -0.145693), (-0.298403, -0.15107, -0.942408)	15.931, 44.759, -67.965

-
Protein , 2 types, 12 molecules ABCDEFQRSTUV

#1: Protein	HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT Mass: 28347.314 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: E1K248, cytochrome-c3 hydrogenase
#2: Protein	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / NIFE-HYDROGENASE LARGE SUBUNIT Mass: 61220.871 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: E1K247, cytochrome-c3 hydrogenase

#1: Protein

HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT

Mass: 28347.314 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
Production host:

DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: E1K248, cytochrome-c3 hydrogenase

#2: Protein

NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / NIFE-HYDROGENASE LARGE SUBUNIT

Mass: 61220.871 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
Production host:

DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: E1K247, cytochrome-c3 hydrogenase

-
Non-polymers , 10 types, 3473 molecules

#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Chemical	ChemComp-F3S / FE3-S4 CLUSTER Mass: 295.795 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe₃S₄
#5: Chemical	ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON Mass: 135.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃FeN₂O
#6: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#7: Chemical	ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H₂S
#8: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#9: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#10: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#11: Chemical	ChemComp-CO3 / CARBONATE ION Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO₃
#12: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3410 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y
Sequence details	N-TERMINAL STREP TAG

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 42 % / Description: NONE
Crystal grow	pH: 6.3 / Details: INSIDE ANAEROBIC GLOVE BOX, PEG6000, MES, PH 7.3

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9395 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. obs: 414223 / % possible obs: 85 % / Redundancy: 1.9 % / R_merge(I) obs: 0.05 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 75.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw

Resolution: 1.7→20 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.95 / SU B: 5.452 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18539	20971	5.1 %	RANDOM
R_work	0.13659	-	-	-
obs	0.13905	393108	84.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 21.001 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	-1.07 Å²	-0.12 Å²
2-	-	0.04 Å²	0.1 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	36866	0	272	3410	40548

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	38666
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.421	1.977	52339
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.932	5	4829
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.05	24.489	1566
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.622	15	6288
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.398	15	145
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	5768
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	28855
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.601	1.897	19346
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.841	3.555	24165
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.242	2.049	19320
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	2.705		38666
X-RAY DIFFRACTION	r_sphericity_free	22.467	5	1063
X-RAY DIFFRACTION	r_sphericity_bonded	15.09		39891

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	226	medium positional	0.06	0.2
1	2	B	226	medium positional	0.05	0.2
1	3	C	226	medium positional	0.06	0.2
1	4	D	226	medium positional	0.05	0.2
1	5	E	226	medium positional	0.06	0.2
1	6	F	226	medium positional	0.06	0.2
2	1	A	83	medium positional	0.06	0.2
2	2	B	83	medium positional	0.06	0.2
2	3	C	83	medium positional	0.06	0.2
2	4	D	83	medium positional	0.06	0.2
2	5	E	83	medium positional	0.06	0.2
2	6	F	83	medium positional	0.06	0.2
3	1	A	163	medium positional	0.05	0.2
3	2	B	163	medium positional	0.06	0.2
3	3	C	163	medium positional	0.05	0.2
3	4	D	163	medium positional	0.05	0.2
3	5	E	163	medium positional	0.06	0.2
3	6	F	163	medium positional	0.05	0.2
5	1	Q	441	medium positional	0.05	0.2
5	2	R	441	medium positional	0.06	0.2
5	3	S	441	medium positional	0.05	0.2
5	4	T	441	medium positional	0.05	0.2
5	5	U	441	medium positional	0.06	0.2
5	6	V	441	medium positional	0.05	0.2
6	1	Q	274	medium positional	0.05	0.2
6	2	R	274	medium positional	0.05	0.2
6	3	S	274	medium positional	0.06	0.2
6	4	T	274	medium positional	0.05	0.2
6	5	U	274	medium positional	0.05	0.2
6	6	V	274	medium positional	0.06	0.2
7	1	Q	230	medium positional	0.05	0.2
7	2	R	230	medium positional	0.05	0.2
7	3	S	230	medium positional	0.06	0.2
7	4	T	230	medium positional	0.05	0.2
7	5	U	230	medium positional	0.05	0.2
7	6	V	230	medium positional	0.05	0.2
8	1	Q	246	medium positional	0.06	0.2
8	2	R	246	medium positional	0.06	0.2
8	3	S	246	medium positional	0.06	0.2
8	4	T	246	medium positional	0.06	0.2
8	5	U	246	medium positional	0.05	0.2
8	6	V	246	medium positional	0.06	0.2
9	1	Q	346	medium positional	0.05	0.2
9	2	R	346	medium positional	0.07	0.2
9	3	S	346	medium positional	0.06	0.2
9	4	T	346	medium positional	0.05	0.2
9	5	U	346	medium positional	0.06	0.2
9	6	V	346	medium positional	0.06	0.2
1	1	A	346	tight thermal	4.02	3
1	2	B	346	tight thermal	3.67	3
1	3	C	346	tight thermal	5.73	3
1	4	D	346	tight thermal	3.98	3
1	5	E	346	tight thermal	4.39	3
1	6	F	346	tight thermal	4.14	3
2	1	A	202	tight thermal	3.84	3
2	2	B	202	tight thermal	5.74	3
2	3	C	202	tight thermal	6.4	3
2	4	D	202	tight thermal	4.03	3
2	5	E	202	tight thermal	6.96	3
2	6	F	202	tight thermal	4.47	3
3	1	A	429	tight thermal	6.39	3
3	2	B	429	tight thermal	12.56	3
3	3	C	429	tight thermal	8.19	3
3	4	D	429	tight thermal	5.81	3
3	5	E	429	tight thermal	12.45	3
3	6	F	429	tight thermal	6.85	3
4	1	Q	195	tight thermal	3.7	3
4	2	R	195	tight thermal	3.23	3
4	3	S	195	tight thermal	4.89	3
4	4	T	195	tight thermal	3.65	3
4	5	U	195	tight thermal	3.16	3
4	6	V	195	tight thermal	3.79	3
5	1	Q	476	tight thermal	4.53	3
5	2	R	476	tight thermal	5.13	3
5	3	S	476	tight thermal	6.41	3
5	4	T	476	tight thermal	4.32	3
5	5	U	476	tight thermal	5.16	3
5	6	V	476	tight thermal	6.37	3
6	1	Q	324	tight thermal	4.5	3
6	2	R	324	tight thermal	6.15	3
6	3	S	324	tight thermal	6.91	3
6	4	T	324	tight thermal	4.31	3
6	5	U	324	tight thermal	6.21	3
6	6	V	324	tight thermal	6.69	3
7	1	Q	280	tight thermal	4.93	3
7	2	R	280	tight thermal	7.27	3
7	3	S	280	tight thermal	6.96	3
7	4	T	280	tight thermal	4.35	3
7	5	U	280	tight thermal	6.17	3
7	6	V	280	tight thermal	8.73	3
8	1	Q	252	tight thermal	4.74	3
8	2	R	252	tight thermal	6.8	3
8	3	S	252	tight thermal	8.1	3
8	4	T	252	tight thermal	4.68	3
8	5	U	252	tight thermal	5.44	3
8	6	V	252	tight thermal	8.96	3
9	1	Q	396	tight thermal	4.92	3
9	2	R	396	tight thermal	5.71	3
9	3	S	396	tight thermal	6.77	3
9	4	T	396	tight thermal	4.35	3
9	5	U	396	tight thermal	4.96	3
9	6	V	396	tight thermal	7.46	3
1	1	A	226	medium thermal	4.32	6
1	2	B	226	medium thermal	4.32	6
1	3	C	226	medium thermal	6.12	6
1	4	D	226	medium thermal	4.34	6
1	5	E	226	medium thermal	4.84	6
1	6	F	226	medium thermal	4.88	6
2	1	A	83	medium thermal	4.32	6
2	2	B	83	medium thermal	6.23	6
2	3	C	83	medium thermal	6.65	6
2	4	D	83	medium thermal	4.38	6
2	5	E	83	medium thermal	7.52	6
2	6	F	83	medium thermal	4.96	6
3	1	A	163	medium thermal	6.86	6
3	2	B	163	medium thermal	12.7	6
3	3	C	163	medium thermal	8.01	6
3	4	D	163	medium thermal	6.25	6
3	5	E	163	medium thermal	12.45	6
3	6	F	163	medium thermal	6.67	6
5	1	Q	441	medium thermal	4.72	6
5	2	R	441	medium thermal	5.21	6
5	3	S	441	medium thermal	6.41	6
5	4	T	441	medium thermal	4.45	6
5	5	U	441	medium thermal	5.06	6
5	6	V	441	medium thermal	6.32	6
6	1	Q	274	medium thermal	4.93	6
6	2	R	274	medium thermal	6.33	6
6	3	S	274	medium thermal	7.22	6
6	4	T	274	medium thermal	4.74	6
6	5	U	274	medium thermal	6.47	6
6	6	V	274	medium thermal	6.95	6
7	1	Q	230	medium thermal	5.07	6
7	2	R	230	medium thermal	6.86	6
7	3	S	230	medium thermal	6.91	6
7	4	T	230	medium thermal	4.68	6
7	5	U	230	medium thermal	6.14	6
7	6	V	230	medium thermal	8.32	6
8	1	Q	246	medium thermal	4.93	6
8	2	R	246	medium thermal	6.58	6
8	3	S	246	medium thermal	7.89	6
8	4	T	246	medium thermal	4.67	6
8	5	U	246	medium thermal	5.32	6
8	6	V	246	medium thermal	8.55	6
9	1	Q	346	medium thermal	5.02	6
9	2	R	346	medium thermal	5.71	6
9	3	S	346	medium thermal	6.8	6
9	4	T	346	medium thermal	4.55	6
9	5	U	346	medium thermal	5.09	6
9	6	V	346	medium thermal	7.26	6

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	1231	-
R_work	0.213	23953	-
obs	-	-	70.15 %

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