PDB-3h3x: Structure of the V74M large subunit mutant of NI-FE hydrogenase i...

ID or keywords:

Entry

Database: PDB / ID: 3h3x

Title

Structure of the V74M large subunit mutant of NI-FE hydrogenase in an oxidized state

Components

(Periplasmic [NiFe] hydrogenase ...) x 2

Keywords

OXIDOREDUCTASE / NI-FE HYDROGENASE TUNNEL MUTANT /

NICKEL /

IRON /

Iron-sulfur / Metal-binding

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

Biological species

Desulfovibrio fructosovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Volbeda, A. / Martinez, N. / Martin, L. / Fontecilla-Camps, J.C.

Citation

Journal: J.Am.Chem.Soc. / Year: 2009
Title: Introduction of methionines in the gas channel makes [NiFe] hydrogenase aero-tolerant
Authors: Dementin, S. / Leroux, F. / Cournac, L. / de Lacey, A.L. / Volbeda, A. / Leger, C. / Burlat, B. / Martinez, N. / Champ, S. / Martin, L. / Sanganas, O. / Haumann, M. / Fernandez, V.M. / ...

History

Deposition	Apr 17, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 21, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Mar 7, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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_asym_id / _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_asym_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_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3x ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3x	HTTPS FTP

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Related structure data

Related structure data	1yqwS 1frf 1yrq 3cur 3cus S: Starting model for refinement
Similar structure data	4uew-2 4ucw-1 1yrq-2 4upe-2 1yqw-1 3cur-3 3cur-2 1yrq-6 4ue2-1 4ud6-3 4ucq-2 1yrq-4 1yrq-5 1e3d-1 3cus-2 4ud2-3 3cur-1 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

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) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Periplasmic [NiFe] hydrogenase small subunit

Q: Periplasmic [NiFe] hydrogenase large subunit

B: Periplasmic [NiFe] hydrogenase small subunit

R: Periplasmic [NiFe] hydrogenase large subunit

C: Periplasmic [NiFe] hydrogenase small subunit

S: Periplasmic [NiFe] hydrogenase large subunit

hetero molecules

269 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Periplasmic [NiFe] hydrogenase small subunit

Q: Periplasmic [NiFe] hydrogenase large subunit

hetero molecules

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

2

B: Periplasmic [NiFe] hydrogenase small subunit

R: Periplasmic [NiFe] hydrogenase large subunit

hetero molecules

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

3

C: Periplasmic [NiFe] hydrogenase small subunit

S: Periplasmic [NiFe] hydrogenase large subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.400, 99.200, 182.300
Angle α, β, γ (deg.)	90.00, 92.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C
1	3	Q
2	3	R
3	3	S
1	4	Q
2	4	R
3	4	S

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	PRO	PRO	3	A	A	7	7
2	1	1	PRO	PRO	PRO	PRO	3	B	C	7	7
3	1	1	PRO	PRO	PRO	PRO	3	C	E	7	7
1	2	1	SER	SER	ILE	ILE	1	A	A	8 - 28	8 - 28
2	2	1	SER	SER	ILE	ILE	1	B	C	8 - 28	8 - 28
3	2	1	SER	SER	ILE	ILE	1	C	E	8 - 28	8 - 28
1	3	1	LYS	LYS	PRO	PRO	3	A	A	29 - 30	29 - 30
2	3	1	LYS	LYS	PRO	PRO	3	B	C	29 - 30	29 - 30
3	3	1	LYS	LYS	PRO	PRO	3	C	E	29 - 30	29 - 30
1	4	1	TYR	TYR	ILE	ILE	1	A	A	31 - 36	31 - 36
2	4	1	TYR	TYR	ILE	ILE	1	B	C	31 - 36	31 - 36
3	4	1	TYR	TYR	ILE	ILE	1	C	E	31 - 36	31 - 36
1	5	1	LEU	LEU	THR	THR	3	A	A	37 - 39	37 - 39
2	5	1	LEU	LEU	THR	THR	3	B	C	37 - 39	37 - 39
3	5	1	LEU	LEU	THR	THR	3	C	E	37 - 39	37 - 39
1	6	1	ILE	ILE	GLY	GLY	1	A	A	40 - 53	40 - 53
2	6	1	ILE	ILE	GLY	GLY	1	B	C	40 - 53	40 - 53
3	6	1	ILE	ILE	GLY	GLY	1	C	E	40 - 53	40 - 53
1	7	1	GLU	GLU	GLU	GLU	3	A	A	54	54
2	7	1	GLU	GLU	GLU	GLU	3	B	C	54	54
3	7	1	GLU	GLU	GLU	GLU	3	C	E	54	54
1	8	1	ALA	ALA	ALA	ALA	4	A	A	55	55
2	8	1	ALA	ALA	ALA	ALA	4	B	C	55	55
3	8	1	ALA	ALA	ALA	ALA	4	C	E	55	55
1	9	1	ALA	ALA	GLU	GLU	1	A	A	56 - 57	56 - 57
2	9	1	ALA	ALA	GLU	GLU	1	B	C	56 - 57	56 - 57
3	9	1	ALA	ALA	GLU	GLU	1	C	E	56 - 57	56 - 57
1	10	1	ALA	ALA	ALA	ALA	4	A	A	58	58
2	10	1	ALA	ALA	ALA	ALA	4	B	C	58	58
3	10	1	ALA	ALA	ALA	ALA	4	C	E	58	58
1	11	1	ALA	ALA	LEU	LEU	1	A	A	59 - 60	59 - 60
2	11	1	ALA	ALA	LEU	LEU	1	B	C	59 - 60	59 - 60
3	11	1	ALA	ALA	LEU	LEU	1	C	E	59 - 60	59 - 60
1	12	1	GLN	GLN	GLN	GLN	2	A	A	62	62
2	12	1	GLN	GLN	GLN	GLN	2	B	C	62	62
3	12	1	GLN	GLN	GLN	GLN	2	C	E	62	62
1	13	1	ALA	ALA	LEU	LEU	1	A	A	63 - 64	63 - 64
2	13	1	ALA	ALA	LEU	LEU	1	B	C	63 - 64	63 - 64
3	13	1	ALA	ALA	LEU	LEU	1	C	E	63 - 64	63 - 64
1	14	1	GLU	GLU	ASP	ASP	3	A	A	65 - 68	65 - 68
2	14	1	GLU	GLU	ASP	ASP	3	B	C	65 - 68	65 - 68
3	14	1	GLU	GLU	ASP	ASP	3	C	E	65 - 68	65 - 68
1	15	1	GLY	GLY	TYR	TYR	1	A	A	69 - 70	69 - 70
2	15	1	GLY	GLY	TYR	TYR	1	B	C	69 - 70	69 - 70
3	15	1	GLY	GLY	TYR	TYR	1	C	E	69 - 70	69 - 70
1	16	1	TYR	TYR	TYR	TYR	2	A	A	71	71
2	16	1	TYR	TYR	TYR	TYR	2	B	C	71	71
3	16	1	TYR	TYR	TYR	TYR	2	C	E	71	71
1	17	1	LEU	LEU	ILE	ILE	1	A	A	72 - 81	72 - 81
2	17	1	LEU	LEU	ILE	ILE	1	B	C	72 - 81	72 - 81
3	17	1	LEU	LEU	ILE	ILE	1	C	E	72 - 81	72 - 81
1	18	1	ASP	ASP	GLN	GLN	3	A	A	82 - 85	82 - 85
2	18	1	ASP	ASP	GLN	GLN	3	B	C	82 - 85	82 - 85
3	18	1	ASP	ASP	GLN	GLN	3	C	E	82 - 85	82 - 85
1	19	1	TRP	TRP	GLY	GLY	1	A	A	86 - 91	86 - 91
2	19	1	TRP	TRP	GLY	GLY	1	B	C	86 - 91	86 - 91
3	19	1	TRP	TRP	GLY	GLY	1	C	E	86 - 91	86 - 91
1	20	1	HIS	HIS	HIS	HIS	3	A	A	92	92
2	20	1	HIS	HIS	HIS	HIS	3	B	C	92	92
3	20	1	HIS	HIS	HIS	HIS	3	C	E	92	92
1	21	1	PRO	PRO	MET	MET	1	A	A	93 - 94	93 - 94
2	21	1	PRO	PRO	MET	MET	1	B	C	93 - 94	93 - 94
3	21	1	PRO	PRO	MET	MET	1	C	E	93 - 94	93 - 94
1	22	1	ILE	ILE	LYS	LYS	3	A	A	95 - 99	95 - 99
2	22	1	ILE	ILE	LYS	LYS	3	B	C	95 - 99	95 - 99
3	22	1	ILE	ILE	LYS	LYS	3	C	E	95 - 99	95 - 99
1	23	1	ALA	ALA	ALA	ALA	1	A	A	101	101
2	23	1	ALA	ALA	ALA	ALA	1	B	C	101	101
3	23	1	ALA	ALA	ALA	ALA	1	C	E	101	101
1	24	1	LYS	LYS	LYS	LYS	3	A	A	104	104
2	24	1	LYS	LYS	LYS	LYS	3	B	C	104	104
3	24	1	LYS	LYS	LYS	LYS	3	C	E	104	104
1	25	1	ALA	ALA	ALA	ALA	4	A	A	105	105
2	25	1	ALA	ALA	ALA	ALA	4	B	C	105	105
3	25	1	ALA	ALA	ALA	ALA	4	C	E	105	105
1	26	1	LYS	LYS	LYS	LYS	3	A	A	106	106
2	26	1	LYS	LYS	LYS	LYS	3	B	C	106	106
3	26	1	LYS	LYS	LYS	LYS	3	C	E	106	106
1	27	1	GLY	GLY	ALA	ALA	1	A	A	107 - 130	107 - 130
2	27	1	GLY	GLY	ALA	ALA	1	B	C	107 - 130	107 - 130
3	27	1	GLY	GLY	ALA	ALA	1	C	E	107 - 130	107 - 130
1	28	1	LYS	LYS	LYS	LYS	2	A	A	131	131
2	28	1	LYS	LYS	LYS	LYS	2	B	C	131	131
3	28	1	LYS	LYS	LYS	LYS	2	C	E	131	131
1	29	1	GLY	GLY	VAL	VAL	1	A	A	132 - 133	132 - 133
2	29	1	GLY	GLY	VAL	VAL	1	B	C	132 - 133	132 - 133
3	29	1	GLY	GLY	VAL	VAL	1	C	E	132 - 133	132 - 133
1	30	1	THR	THR	VAL	VAL	1	A	A	141 - 159	141 - 159
2	30	1	THR	THR	VAL	VAL	1	B	C	141 - 159	141 - 159
3	30	1	THR	THR	VAL	VAL	1	C	E	141 - 159	141 - 159
1	31	1	HIS	HIS	HIS	HIS	2	A	A	160	160
2	31	1	HIS	HIS	HIS	HIS	2	B	C	160	160
3	31	1	HIS	HIS	HIS	HIS	2	C	E	160	160
1	32	1	VAL	VAL	LEU	LEU	3	A	A	161 - 162	161 - 162
2	32	1	VAL	VAL	LEU	LEU	3	B	C	161 - 162	161 - 162
3	32	1	VAL	VAL	LEU	LEU	3	C	E	161 - 162	161 - 162
1	33	1	THR	THR	THR	THR	6	A	A	163	163
2	33	1	THR	THR	THR	THR	6	B	C	163	163
3	33	1	THR	THR	THR	THR	6	C	E	163	163
1	34	1	LYS	LYS	LYS	LYS	3	A	A	164	164
2	34	1	LYS	LYS	LYS	LYS	3	B	C	164	164
3	34	1	LYS	LYS	LYS	LYS	3	C	E	164	164
1	35	1	GLY	GLY	PRO	PRO	2	A	A	165 - 167	165 - 167
2	35	1	GLY	GLY	PRO	PRO	2	B	C	165 - 167	165 - 167
3	35	1	GLY	GLY	PRO	PRO	2	C	E	165 - 167	165 - 167
1	36	1	ASP	ASP	LEU	LEU	3	A	A	168 - 169	168 - 169
2	36	1	ASP	ASP	LEU	LEU	3	B	C	168 - 169	168 - 169
3	36	1	ASP	ASP	LEU	LEU	3	C	E	168 - 169	168 - 169
1	37	1	ASP	ASP	GLU	GLU	6	A	A	170 - 171	170 - 171
2	37	1	ASP	ASP	GLU	GLU	6	B	C	170 - 171	170 - 171
3	37	1	ASP	ASP	GLU	GLU	6	C	E	170 - 171	170 - 171
1	38	1	SF4	SF4	SF4	SF4	1	A	I	267
2	38	1	SF4	SF4	SF4	SF4	1	B	R	267
3	38	1	SF4	SF4	SF4	SF4	1	C	AA	267
1	1	2	GLY	GLY	PRO	PRO	1	A	A	173 - 175	173 - 175
2	1	2	GLY	GLY	PRO	PRO	1	B	C	173 - 175	173 - 175
3	1	2	GLY	GLY	PRO	PRO	1	C	E	173 - 175	173 - 175
1	2	2	LYS	LYS	LEU	LEU	3	A	A	176 - 177	176 - 177
2	2	2	LYS	LYS	LEU	LEU	3	B	C	176 - 177	176 - 177
3	2	2	LYS	LYS	LEU	LEU	3	C	E	176 - 177	176 - 177
1	3	2	PHE	PHE	TYR	TYR	1	A	A	178 - 179	178 - 179
2	3	2	PHE	PHE	TYR	TYR	1	B	C	178 - 179	178 - 179
3	3	2	PHE	PHE	TYR	TYR	1	C	E	178 - 179	178 - 179
1	4	2	GLY	GLY	LEU	LEU	3	A	A	180 - 182	180 - 182
2	4	2	GLY	GLY	LEU	LEU	3	B	C	180 - 182	180 - 182
3	4	2	GLY	GLY	LEU	LEU	3	C	E	180 - 182	180 - 182
1	5	2	VAL	VAL	CYS	CYS	1	A	A	183 - 187	183 - 187
2	5	2	VAL	VAL	CYS	CYS	1	B	C	183 - 187	183 - 187
3	5	2	VAL	VAL	CYS	CYS	1	C	E	183 - 187	183 - 187
1	6	2	PRO	PRO	LEU	LEU	2	A	A	188 - 190	188 - 190
2	6	2	PRO	PRO	LEU	LEU	2	B	C	188 - 190	188 - 190
3	6	2	PRO	PRO	LEU	LEU	2	C	E	188 - 190	188 - 190
1	7	2	PRO	PRO	GLU	GLU	3	A	A	191 - 194	191 - 194
2	7	2	PRO	PRO	GLU	GLU	3	B	C	191 - 194	191 - 194
3	7	2	PRO	PRO	GLU	GLU	3	C	E	191 - 194	191 - 194
1	8	2	ALA	ALA	SER	SER	2	A	A	195 - 196	195 - 196
2	8	2	ALA	ALA	SER	SER	2	B	C	195 - 196	195 - 196
3	8	2	ALA	ALA	SER	SER	2	C	E	195 - 196	195 - 196
1	9	2	GLU	GLU	PHE	PHE	3	A	A	197 - 198	197 - 198
2	9	2	GLU	GLU	PHE	PHE	3	B	C	197 - 198	197 - 198
3	9	2	GLU	GLU	PHE	PHE	3	C	E	197 - 198	197 - 198
1	10	2	ALA	ALA	PHE	PHE	1	A	A	199 - 202	199 - 202
2	10	2	ALA	ALA	PHE	PHE	1	B	C	199 - 202	199 - 202
3	10	2	ALA	ALA	PHE	PHE	1	C	E	199 - 202	199 - 202
1	11	2	ASP	ASP	ASP	ASP	3	A	A	203	203
2	11	2	ASP	ASP	ASP	ASP	3	B	C	203	203
3	11	2	ASP	ASP	ASP	ASP	3	C	E	203	203
1	12	2	SER	SER	SER	SER	1	A	A	204	204
2	12	2	SER	SER	SER	SER	1	B	C	204	204
3	12	2	SER	SER	SER	SER	1	C	E	204	204
1	13	2	GLU	GLU	GLU	GLU	3	A	A	205 - 206	205 - 206
2	13	2	GLU	GLU	GLU	GLU	3	B	C	205 - 206	205 - 206
3	13	2	GLU	GLU	GLU	GLU	3	C	E	205 - 206	205 - 206
1	14	2	ALA	ALA	LYS	LYS	1	A	A	207 - 208	207 - 208
2	14	2	ALA	ALA	LYS	LYS	1	B	C	207 - 208	207 - 208
3	14	2	ALA	ALA	LYS	LYS	1	C	E	207 - 208	207 - 208
1	15	2	LYS	LYS	LYS	LYS	3	A	A	209	209
2	15	2	LYS	LYS	LYS	LYS	3	B	C	209	209
3	15	2	LYS	LYS	LYS	LYS	3	C	E	209	209
1	16	2	GLY	GLY	LEU	LEU	1	A	A	210 - 213	210 - 213
2	16	2	GLY	GLY	LEU	LEU	1	B	C	210 - 213	210 - 213
3	16	2	GLY	GLY	LEU	LEU	1	C	E	210 - 213	210 - 213
1	17	2	TYR	TYR	GLU	GLU	3	A	A	214 - 215	214 - 215
2	17	2	TYR	TYR	GLU	GLU	3	B	C	214 - 215	214 - 215
3	17	2	TYR	TYR	GLU	GLU	3	C	E	214 - 215	214 - 215
1	18	2	LEU	LEU	GLY	GLY	1	A	A	216 - 220	216 - 220
2	18	2	LEU	LEU	GLY	GLY	1	B	C	216 - 220	216 - 220
3	18	2	LEU	LEU	GLY	GLY	1	C	E	216 - 220	216 - 220
1	19	2	PRO	PRO	PRO	PRO	2	A	A	221	221
2	19	2	PRO	PRO	PRO	PRO	2	B	C	221	221
3	19	2	PRO	PRO	PRO	PRO	2	C	E	221	221
1	20	2	VAL	VAL	PRO	PRO	1	A	A	222 - 228	222 - 228
2	20	2	VAL	VAL	PRO	PRO	1	B	C	222 - 228	222 - 228
3	20	2	VAL	VAL	PRO	PRO	1	C	E	222 - 228	222 - 228
1	21	2	LYS	LYS	LYS	LYS	3	A	A	229	229
2	21	2	LYS	LYS	LYS	LYS	3	B	C	229	229
3	21	2	LYS	LYS	LYS	LYS	3	C	E	229	229
1	22	2	VAL	VAL	ASN	ASN	1	A	A	230 - 233	230 - 233
2	22	2	VAL	VAL	ASN	ASN	1	B	C	230 - 233	230 - 233
3	22	2	VAL	VAL	ASN	ASN	1	C	E	230 - 233	230 - 233
1	23	2	GLN	GLN	GLN	GLN	2	A	A	234	234
2	23	2	GLN	GLN	GLN	GLN	2	B	C	234	234
3	23	2	GLN	GLN	GLN	GLN	2	C	E	234	234
1	24	2	VAL	VAL	TRP	TRP	1	A	A	235 - 254	235 - 254
2	24	2	VAL	VAL	TRP	TRP	1	B	C	235 - 254	235 - 254
3	24	2	VAL	VAL	TRP	TRP	1	C	E	235 - 254	235 - 254
1	25	2	ASP	ASP	ASP	ASP	4	A	A	255	255
2	25	2	ASP	ASP	ASP	ASP	4	B	C	255	255
3	25	2	ASP	ASP	ASP	ASP	4	C	E	255	255
1	26	2	THR	THR	THR	THR	1	A	A	256 - 258	256 - 258
2	26	2	THR	THR	THR	THR	1	B	C	256 - 258	256 - 258
3	26	2	THR	THR	THR	THR	1	C	E	256 - 258	256 - 258
1	27	2	PRO	PRO	PRO	PRO	2	A	A	259	259
2	27	2	PRO	PRO	PRO	PRO	2	B	C	259	259
3	27	2	PRO	PRO	PRO	PRO	2	C	E	259	259
1	28	2	PHE	PHE	TYR	TYR	1	A	A	260 - 261	260 - 261
2	28	2	PHE	PHE	TYR	TYR	1	B	C	260 - 261	260 - 261
3	28	2	PHE	PHE	TYR	TYR	1	C	E	260 - 261	260 - 261
1	29	2	SF4	SF4	F3S	F3S	1	A	G - H	265 - 266
2	29	2	SF4	SF4	F3S	F3S	1	B	P - Q	265 - 266
3	29	2	SF4	SF4	F3S	F3S	1	C	Y - Z	265 - 266
1	1	3	THR	THR	GLY	GLY	3	Q	B	7 - 14	7 - 14
2	1	3	THR	THR	GLY	GLY	3	R	D	7 - 14	7 - 14
3	1	3	THR	THR	GLY	GLY	3	S	F	7 - 14	7 - 14
1	2	3	PRO	PRO	VAL	VAL	1	Q	B	15 - 32	15 - 32
2	2	3	PRO	PRO	VAL	VAL	1	R	D	15 - 32	15 - 32
3	2	3	PRO	PRO	VAL	VAL	1	S	F	15 - 32	15 - 32
1	3	3	GLU	GLU	LYS	LYS	3	Q	B	33 - 40	33 - 40
2	3	3	GLU	GLU	LYS	LYS	3	R	D	33 - 40	33 - 40
3	3	3	GLU	GLU	LYS	LYS	3	S	F	33 - 40	33 - 40
1	4	3	ASP	ASP	LEU	LEU	1	Q	B	41 - 56	41 - 56
2	4	3	ASP	ASP	LEU	LEU	1	R	D	41 - 56	41 - 56
3	4	3	ASP	ASP	LEU	LEU	1	S	F	41 - 56	41 - 56
1	5	3	LYS	LYS	LYS	LYS	3	Q	B	57	57
2	5	3	LYS	LYS	LYS	LYS	3	R	D	57	57
3	5	3	LYS	LYS	LYS	LYS	3	S	F	57	57
1	6	3	GLY	GLY	PRO	PRO	1	Q	B	58 - 61	58 - 61
2	6	3	GLY	GLY	PRO	PRO	1	R	D	58 - 61	58 - 61
3	6	3	GLY	GLY	PRO	PRO	1	S	F	58 - 61	58 - 61
1	7	3	ARG	ARG	ARG	ARG	3	Q	B	62	62
2	7	3	ARG	ARG	ARG	ARG	3	R	D	62	62
3	7	3	ARG	ARG	ARG	ARG	3	S	F	62	62
1	8	3	GLY	GLY	VAL	VAL	1	Q	B	58 - 91	58 - 91
2	8	3	GLY	GLY	VAL	VAL	1	R	D	58 - 91	58 - 91
3	8	3	GLY	GLY	VAL	VAL	1	S	F	58 - 91	58 - 91
1	9	3	LYS	LYS	SER	SER	3	Q	B	92 - 94	92 - 94
2	9	3	LYS	LYS	SER	SER	3	R	D	92 - 94	92 - 94
3	9	3	LYS	LYS	SER	SER	3	S	F	92 - 94	92 - 94
1	10	3	ILE	ILE	HIS	HIS	1	Q	B	95 - 115	95 - 115
2	10	3	ILE	ILE	HIS	HIS	1	R	D	95 - 115	95 - 115
3	10	3	ILE	ILE	HIS	HIS	1	S	F	95 - 115	95 - 115
1	11	3	LEU	LEU	LEU	LEU	3	Q	B	116	116
2	11	3	LEU	LEU	LEU	LEU	3	R	D	116	116
3	11	3	LEU	LEU	LEU	LEU	3	S	F	116	116
1	12	3	VAL	VAL	VAL	VAL	1	Q	B	117 - 130	117 - 130
2	12	3	VAL	VAL	VAL	VAL	1	R	D	117 - 130	117 - 130
3	12	3	VAL	VAL	VAL	VAL	1	S	F	117 - 130	117 - 130
1	13	3	THR	THR	ALA	ALA	5	Q	B	131 - 133	131 - 133
2	13	3	THR	THR	ALA	ALA	5	R	D	131 - 133	131 - 133
3	13	3	THR	THR	ALA	ALA	5	S	F	131 - 133	131 - 133
1	14	3	ALA	ALA	ALA	ALA	4	Q	B	141 - 142	141 - 142
2	14	3	ALA	ALA	ALA	ALA	4	R	D	141 - 142	141 - 142
3	14	3	ALA	ALA	ALA	ALA	4	S	F	141 - 142	141 - 142
1	15	3	ALA	ALA	ALA	ALA	3	Q	B	151 - 159	151 - 159
2	15	3	ALA	ALA	ALA	ALA	3	R	D	151 - 159	151 - 159
3	15	3	ALA	ALA	ALA	ALA	3	S	F	151 - 159	151 - 159
1	16	3	LYS	LYS	LEU	LEU	3	Q	B	161 - 176	161 - 176
2	16	3	LYS	LYS	LEU	LEU	3	R	D	161 - 176	161 - 176
3	16	3	LYS	LYS	LEU	LEU	3	S	F	161 - 176	161 - 176
1	17	3	GLY	GLY	THR	THR	1	Q	B	177 - 180	177 - 180
2	17	3	GLY	GLY	THR	THR	1	R	D	177 - 180	177 - 180
3	17	3	GLY	GLY	THR	THR	1	S	F	177 - 180	177 - 180
1	18	3	ASN	ASN	LEU	LEU	3	Q	B	181 - 185	181 - 185
2	18	3	ASN	ASN	LEU	LEU	3	R	D	181 - 185	181 - 185
3	18	3	ASN	ASN	LEU	LEU	3	S	F	181 - 185	181 - 185
1	19	3	ALA	ALA	GLU	GLU	3	Q	B	190 - 196	190 - 196
2	19	3	ALA	ALA	GLU	GLU	3	R	D	190 - 196	190 - 196
3	19	3	ALA	ALA	GLU	GLU	3	S	F	190 - 196	190 - 196
1	20	3	VAL	VAL	TYR	TYR	1	Q	B	197 - 205	197 - 205
2	20	3	VAL	VAL	TYR	TYR	1	R	D	197 - 205	197 - 205
3	20	3	VAL	VAL	TYR	TYR	1	S	F	197 - 205	197 - 205
1	21	3	LEU	LEU	LYS	LYS	2	Q	B	206 - 214	206 - 214
2	21	3	LEU	LEU	LYS	LYS	2	R	D	206 - 214	206 - 214
3	21	3	LEU	LEU	LYS	LYS	2	S	F	206 - 214	206 - 214
1	22	3	ALA	ALA	TYR	TYR	1	Q	B	215 - 240	215 - 240
2	22	3	ALA	ALA	TYR	TYR	1	R	D	215 - 240	215 - 240
3	22	3	ALA	ALA	TYR	TYR	1	S	F	215 - 240	215 - 240
1	23	3	GLN	GLN	LYS	LYS	3	Q	B	241 - 278	241 - 278
2	23	3	GLN	GLN	LYS	LYS	3	R	D	241 - 278	241 - 278
3	23	3	GLN	GLN	LYS	LYS	3	S	F	241 - 278	241 - 278
1	24	3	ALA	ALA	THR	THR	2	Q	B	415 - 421	415 - 421
2	24	3	ALA	ALA	THR	THR	2	R	D	415 - 421	415 - 421
3	24	3	ALA	ALA	THR	THR	2	S	F	415 - 421	415 - 421
1	25	3	LEU	LEU	LEU	LEU	3	Q	B	422	422
2	25	3	LEU	LEU	LEU	LEU	3	R	D	422	422
3	25	3	LEU	LEU	LEU	LEU	3	S	F	422	422
1	26	3	GLY	GLY	MET	MET	1	Q	B	423 - 439	423 - 439
2	26	3	GLY	GLY	MET	MET	1	R	D	423 - 439	423 - 439
3	26	3	GLY	GLY	MET	MET	1	S	F	423 - 439	423 - 439
1	27	3	GLU	GLU	MET	MET	3	Q	B	440 - 446	440 - 446
2	27	3	GLU	GLU	MET	MET	3	R	D	440 - 446	440 - 446
3	27	3	GLU	GLU	MET	MET	3	S	F	440 - 446	440 - 446
1	28	3	LEU	LEU	LYS	LYS	3	Q	B	456 - 467	456 - 467
2	28	3	LEU	LEU	LYS	LYS	3	R	D	456 - 467	456 - 467
3	28	3	LEU	LEU	LYS	LYS	3	S	F	456 - 467	456 - 467
1	29	3	GLY	GLY	ILE	ILE	1	Q	B	468 - 483	468 - 483
2	29	3	GLY	GLY	ILE	ILE	1	R	D	468 - 483	468 - 483
3	29	3	GLY	GLY	ILE	ILE	1	S	F	468 - 483	468 - 483
1	30	3	ARG	ARG	ASN	ASN	3	Q	B	484 - 492	484 - 492
2	30	3	ARG	ARG	ASN	ASN	3	R	D	484 - 492	484 - 492
3	30	3	ARG	ARG	ASN	ASN	3	S	F	484 - 492	484 - 492
1	31	3	PHE	PHE	PRO	PRO	1	Q	B	493 - 505	493 - 505
2	31	3	PHE	PHE	PRO	PRO	1	R	D	493 - 505	493 - 505
3	31	3	PHE	PHE	PRO	PRO	1	S	F	493 - 505	493 - 505
1	32	3	ARG	ARG	ILE	ILE	3	Q	B	506 - 520	506 - 520
2	32	3	ARG	ARG	ILE	ILE	3	R	D	506 - 520	506 - 520
3	32	3	ARG	ARG	ILE	ILE	3	S	F	506 - 520	506 - 520
1	33	3	GLY	GLY	ALA	ALA	1	Q	B	521 - 525	521 - 525
2	33	3	GLY	GLY	ALA	ALA	1	R	D	521 - 525	521 - 525
3	33	3	GLY	GLY	ALA	ALA	1	S	F	521 - 525	521 - 525
1	34	3	PRO	PRO	ILE	ILE	1	Q	B	530 - 533	530 - 533
2	34	3	PRO	PRO	ILE	ILE	1	R	D	530 - 533	530 - 533
3	34	3	PRO	PRO	ILE	ILE	1	S	F	530 - 533	530 - 533
1	35	3	LEU	LEU	HIS	HIS	1	Q	B	534 - 549	534 - 549
2	35	3	LEU	LEU	HIS	HIS	1	R	D	534 - 549	534 - 549
3	35	3	LEU	LEU	HIS	HIS	1	S	F	534 - 549	534 - 549
1	36	3	FCO	FCO	MG	MG	1	Q	K - M	550 - 553
2	36	3	FCO	FCO	MG	MG	1	R	S - U	550 - 553
3	36	3	FCO	FCO	MG	MG	1	S	BA - DA	550 - 553
1	1	4	ASP	ASP	ASP	ASP	3	Q	B	279	279
2	1	4	ASP	ASP	ASP	ASP	3	R	D	279	279
3	1	4	ASP	ASP	ASP	ASP	3	S	F	279	279
1	2	4	TRP	TRP	THR	THR	1	Q	B	280 - 286	280 - 286
2	2	4	TRP	TRP	THR	THR	1	R	D	280 - 286	280 - 286
3	2	4	TRP	TRP	THR	THR	1	S	F	280 - 286	280 - 286
1	3	4	SER	SER	ASN	ASN	2	Q	B	287 - 288	287 - 288
2	3	4	SER	SER	ASN	ASN	2	R	D	287 - 288	287 - 288
3	3	4	SER	SER	ASN	ASN	2	S	F	287 - 288	287 - 288
1	4	4	TYR	TYR	ASP	ASP	1	Q	B	289 - 299	289 - 299
2	4	4	TYR	TYR	ASP	ASP	1	R	D	289 - 299	289 - 299
3	4	4	TYR	TYR	ASP	ASP	1	S	F	289 - 299	289 - 299
1	5	4	SER	SER	PRO	PRO	1	Q	B	301 - 302	301 - 302
2	5	4	SER	SER	PRO	PRO	1	R	D	301 - 302	301 - 302
3	5	4	SER	SER	PRO	PRO	1	S	F	301 - 302	301 - 302
1	6	4	LYS	LYS	GLY	GLY	1	Q	B	304 - 318	304 - 318
2	6	4	LYS	LYS	GLY	GLY	1	R	D	304 - 318	304 - 318
3	6	4	LYS	LYS	GLY	GLY	1	S	F	304 - 318	304 - 318
1	7	4	ARG	ARG	LEU	LEU	3	Q	B	319 - 329	319 - 329
2	7	4	ARG	ARG	LEU	LEU	3	R	D	319 - 329	319 - 329
3	7	4	ARG	ARG	LEU	LEU	3	S	F	319 - 329	319 - 329
1	8	4	ALA	ALA	LYS	LYS	3	Q	B	331 - 337	331 - 337
2	8	4	ALA	ALA	LYS	LYS	3	R	D	331 - 337	331 - 337
3	8	4	ALA	ALA	LYS	LYS	3	S	F	331 - 337	331 - 337
1	9	4	TYR	TYR	TYR	TYR	2	Q	B	338 - 341	338 - 341
2	9	4	TYR	TYR	TYR	TYR	2	R	D	338 - 341	338 - 341
3	9	4	TYR	TYR	TYR	TYR	2	S	F	338 - 341	338 - 341
1	10	4	GLY	GLY	GLY	GLY	4	Q	B	345	345
2	10	4	GLY	GLY	GLY	GLY	4	R	D	345	345
3	10	4	GLY	GLY	GLY	GLY	4	S	F	345	345
1	11	4	ASP	ASP	LYS	LYS	3	Q	B	346 - 348	346 - 348
2	11	4	ASP	ASP	LYS	LYS	3	R	D	346 - 348	346 - 348
3	11	4	ASP	ASP	LYS	LYS	3	S	F	346 - 348	346 - 348
1	12	4	HIS	HIS	TYR	TYR	2	Q	B	349 - 351	349 - 351
2	12	4	HIS	HIS	TYR	TYR	2	R	D	349 - 351	349 - 351
3	12	4	HIS	HIS	TYR	TYR	2	S	F	349 - 351	349 - 351
1	13	4	ASP	ASP	TYR	TYR	3	Q	B	352 - 359	352 - 359
2	13	4	ASP	ASP	TYR	TYR	3	R	D	352 - 359	352 - 359
3	13	4	ASP	ASP	TYR	TYR	3	S	F	352 - 359	352 - 359
1	14	4	LYS	LYS	HIS	HIS	3	Q	B	365 - 367	365 - 367
2	14	4	LYS	LYS	HIS	HIS	3	R	D	365 - 367	365 - 367
3	14	4	LYS	LYS	HIS	HIS	3	S	F	365 - 367	365 - 367
1	15	4	TYR	TYR	TYR	TYR	1	Q	B	368 - 376	368 - 376
2	15	4	TYR	TYR	TYR	TYR	1	R	D	368 - 376	368 - 376
3	15	4	TYR	TYR	TYR	TYR	1	S	F	368 - 376	368 - 376
1	16	4	ALA	ALA	ALA	ALA	1	Q	B	380 - 392	380 - 392
2	16	4	ALA	ALA	ALA	ALA	1	R	D	380 - 392	380 - 392
3	16	4	ALA	ALA	ALA	ALA	1	S	F	380 - 392	380 - 392
1	17	4	TYR	TYR	TYR	TYR	2	Q	B	393	393
2	17	4	TYR	TYR	TYR	TYR	2	R	D	393	393
3	17	4	TYR	TYR	TYR	TYR	2	S	F	393	393
1	18	4	ALA	ALA	LYS	LYS	3	Q	B	394 - 395	394 - 395
2	18	4	ALA	ALA	LYS	LYS	3	R	D	394 - 395	394 - 395
3	18	4	ALA	ALA	LYS	LYS	3	S	F	394 - 395	394 - 395
1	19	4	GLY	GLY	PHE	PHE	2	Q	B	396 - 400	396 - 400
2	19	4	GLY	GLY	PHE	PHE	2	R	D	396 - 400	396 - 400
3	19	4	GLY	GLY	PHE	PHE	2	S	F	396 - 400	396 - 400
1	20	4	LYS	LYS	LYS	LYS	3	Q	B	401	401
2	20	4	LYS	LYS	LYS	LYS	3	R	D	401	401
3	20	4	LYS	LYS	LYS	LYS	3	S	F	401	401
1	21	4	VAL	VAL	LEU	LEU	5	Q	B	407 - 408	407 - 408
2	21	4	VAL	VAL	LEU	LEU	5	R	D	407 - 408	407 - 408
3	21	4	VAL	VAL	LEU	LEU	5	S	F	407 - 408	407 - 408
1	22	4	LEU	LEU	PRO	PRO	3	Q	B	411 - 414	411 - 414
2	22	4	LEU	LEU	PRO	PRO	3	R	D	411 - 414	411 - 414
3	22	4	LEU	LEU	PRO	PRO	3	S	F	411 - 414	411 - 414

NCS ensembles :

ID
1
2
3
4

-
Periplasmic [NiFe] hydrogenase ... , 2 types, 6 molecules ABCQRS

#1: Protein	Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain Mass: 28347.314 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio fructosovorans (bacteria) Strain: DSM 3604 / Gene: hydA / Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein	Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain Mass: 59804.398 Da / Num. of mol.: 3 / Mutation: V74M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio fructosovorans (bacteria) Strain: DSM 3604 / Gene: hydB / Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18188, cytochrome-c3 hydrogenase

#1: Protein

Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain

Mass: 28347.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Desulfovibrio fructosovorans (bacteria)
Strain: DSM 3604 / Gene: hydA / Production host:

DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18187,

cytochrome-c3 hydrogenase

#2: Protein

Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain

Mass: 59804.398 Da / Num. of mol.: 3 / Mutation: V74M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Desulfovibrio fructosovorans (bacteria)
Strain: DSM 3604 / Gene: hydB / Production host:

DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18188,

cytochrome-c3 hydrogenase

-
Non-polymers , 7 types, 587 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.: 7 / 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.: 562 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, GLYCEROL, pH6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 / Wavelength: 0.97623 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2008 / Details: mirrors
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97623 Å / Relative weight: 1
Reflection	Resolution: 2.7→20 Å / Num. all: 61024 / Num. obs: 60250 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.42 % / B_iso Wilson estimate: 42.6 Å² / R_merge(I) obs: 0.051 / R_sym value: 0.051 / Net I/σ(I): 15.18
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 3.07 % / R_merge(I) obs: 0.288 / Mean I/σ(I) obs: 4.31 / Num. unique all: 6288 / R_sym value: 0.288 / % possible all: 98.1

-
Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw

Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.873 / SU B: 29.478 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Because of the limited resolution observed density for a NI-FE bridging ligand is not modeled

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	2935	4.9 %	RANDOM
R_work	0.203	-	-	-
obs	0.206	57315	98.73 %	-
all	-	60250	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.52 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.17 Å²	0 Å²	2.44 Å²
2-	-	-0.96 Å²	0 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18400	0	138	562	19100

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	19101
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.451	1.967	25896
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.013	5	2411
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.532	24.392	765
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.823	15	3029
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.862	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	2823
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14406
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	9525
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	12854
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	1096
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.211	0.2	3
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.242	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.286	0.2	11
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	0.367	1.5	12341
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.563	2	19291
X-RAY DIFFRACTION	r_scbond_it	1.054	3	7732
X-RAY DIFFRACTION	r_scangle_it	1.541	4.5	6524
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	951	tight positional	0.05	0.04
1	2	B	951	tight positional	0.04	0.04
1	3	C	951	tight positional	0.04	0.04
2	1	A	603	tight positional	0.04	0.04
2	2	B	603	tight positional	0.04	0.04
2	3	C	603	tight positional	0.05	0.04
3	1	Q	2252	tight positional	0.05	0.04
3	2	R	2252	tight positional	0.04	0.04
3	3	S	2252	tight positional	0.04	0.04
4	1	Q	653	tight positional	0.04	0.04
4	2	R	653	tight positional	0.04	0.04
4	3	S	653	tight positional	0.04	0.04
1	1	A	46	medium positional	0.3	0.2
1	2	B	46	medium positional	0.25	0.2
1	3	C	46	medium positional	0.47	0.2
2	1	A	36	medium positional	0.24	0.2
2	2	B	36	medium positional	0.18	0.2
2	3	C	36	medium positional	0.18	0.2
3	1	Q	79	medium positional	0.18	0.2
3	2	R	79	medium positional	0.18	0.2
3	3	S	79	medium positional	0.19	0.2
4	1	Q	90	medium positional	0.17	0.2
4	2	R	90	medium positional	0.14	0.2
4	3	S	90	medium positional	0.16	0.2
1	1	A	130	loose positional	0.63	5
1	2	B	130	loose positional	0.66	5
1	3	C	130	loose positional	0.59	5
2	1	A	88	loose positional	0.42	5
2	2	B	88	loose positional	0.55	5
2	3	C	88	loose positional	0.36	5
3	1	Q	551	loose positional	0.47	5
3	2	R	551	loose positional	0.48	5
3	3	S	551	loose positional	0.45	5
4	1	Q	160	loose positional	0.45	5
4	2	R	160	loose positional	0.36	5
4	3	S	160	loose positional	0.43	5
1	1	A	951	tight thermal	0.5	1.5
1	2	B	951	tight thermal	0.45	1.5
1	3	C	951	tight thermal	0.48	1.5
2	1	A	603	tight thermal	0.58	1.5
2	2	B	603	tight thermal	0.48	1.5
2	3	C	603	tight thermal	0.52	1.5
3	1	Q	2252	tight thermal	0.51	1.5
3	2	R	2252	tight thermal	0.49	1.5
3	3	S	2252	tight thermal	0.47	1.5
4	1	Q	653	tight thermal	0.52	1.5
4	2	R	653	tight thermal	0.48	1.5
4	3	S	653	tight thermal	0.43	1.5
1	1	A	46	medium thermal	0.74	3
1	2	B	46	medium thermal	0.79	3
1	3	C	46	medium thermal	0.68	3
2	1	A	36	medium thermal	1.36	3
2	2	B	36	medium thermal	1.16	3
2	3	C	36	medium thermal	1.03	3
3	1	Q	79	medium thermal	1.06	3
3	2	R	79	medium thermal	0.83	3
3	3	S	79	medium thermal	0.85	3
4	1	Q	90	medium thermal	0.98	3
4	2	R	90	medium thermal	0.73	3
4	3	S	90	medium thermal	1.11	3
1	1	A	130	loose thermal	1.04	10
1	2	B	130	loose thermal	1.54	10
1	3	C	130	loose thermal	1.41	10
2	1	A	88	loose thermal	1.41	10
2	2	B	88	loose thermal	1.44	10
2	3	C	88	loose thermal	1.71	10
3	1	Q	551	loose thermal	1.49	10
3	2	R	551	loose thermal	1.38	10
3	3	S	551	loose thermal	1.39	10
4	1	Q	160	loose thermal	1.33	10
4	2	R	160	loose thermal	1.45	10
4	3	S	160	loose thermal	1.54	10

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	205	-
R_work	0.223	4110	-
obs	-	4045	97.96 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.8873	0.2956	-0.0002	1.3614	-0.5027	1.6313	-0.0384	0.162	0.3855	0.1161	-0.0256	-0.0076	-0.2423	0.2231	0.064	-0.2867	-0.0236	-0.033	-0.1825	0.1083	-0.0566	12.2532	14.5094	5.2433
2	1.4337	0.1122	0.4134	0.9897	-0.1324	1.3615	0.0754	0.0253	-0.1549	0.1024	-0.0286	-0.1178	0.142	0.067	-0.0468	-0.3036	0.0128	-0.0399	-0.2416	0.0186	-0.0732	7.2062	-6.8163	15.1122
3	1.1829	-0.0132	-0.0329	1.4569	-0.5121	1.898	-0.2037	0.0345	-0.4551	0.2006	0.0499	0.3662	0.5118	-0.1929	0.1538	0.0481	0.0431	0.1408	-0.0592	0.0428	0.3197	-36.8156	-48.9573	53.6515
4	1.4636	-0.4372	-0.9048	1.3511	0.362	2.4437	-0.1885	-0.253	-0.0537	0.144	0.1293	-0.0375	0.1335	0.4046	0.0592	-0.1821	0.0699	-0.0267	-0.0327	0.0152	0.0002	-20.0599	-32.3737	48.8127
5	2.0707	0.8442	-1.2491	1.7042	-1.2412	3.0605	0.092	0.0783	-0.0297	0.0798	-0.0168	0.1741	0.0251	-0.2726	-0.0753	-0.1183	-0.0034	0.0007	-0.1886	-0.0611	-0.1098	-19.0189	6.3695	61.0398
6	2.4683	0.6255	-0.7717	1.0445	-0.4987	1.2092	0.4525	-0.6029	0.3785	0.4508	-0.3259	0.1259	-0.4294	0.2864	-0.1266	0.1648	-0.171	0.0541	-0.0378	-0.1071	-0.0348	-7.1964	19.1281	77.6761

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 264
2	X-RAY DIFFRACTION	2	Q	6 - 549
3	X-RAY DIFFRACTION	3	B	3 - 264
4	X-RAY DIFFRACTION	4	R	5 - 549
5	X-RAY DIFFRACTION	5	C	5 - 264
6	X-RAY DIFFRACTION	6	S	6 - 549

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