PDB-3git: Crystal structure of a truncated acetyl-CoA synthase

ID or keywords:

Entry

Database: PDB / ID: 3git

Title

Crystal structure of a truncated acetyl-CoA synthase

Components

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

Keywords

TRANSFERASE / acetyltransferase / Carbon dioxide fixation / Iron / Iron-sulfur / Metal-binding / Nickel

Function / homology

Function and homology information

CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / carbon fixation / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Moorella thermoacetica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3 Å

Authors

Volbeda, A. / Darnault, C. / Fontecilla-Camps, J.C.

Citation

Journal: Biochemistry / Year: 2009
Title: Novel domain arrangement in the crystal structure of a truncated acetyl-CoA synthase from Moorella thermoacetica
Authors: Volbeda, A. / Darnault, C. / Tan, X. / Lindahl, P.A. / Fontecilla-Camps, J.C.

History

Deposition	Mar 6, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3git.cif.gz	489.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3git.ent.gz	399.7 KB	Display	PDB format
PDBx/mmJSON format	3git.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3git_validation.pdf.gz	548.2 KB	Display	wwPDB validaton report
Full document	3git_full_validation.pdf.gz	589.8 KB	Display
Data in XML	3git_validation.xml.gz	88.7 KB	Display
Data in CIF	3git_validation.cif.gz	119.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/3git ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3git	HTTPS FTP

-
Related structure data

Related structure data	1oaoS S: Starting model for refinement
Similar structure data	3n4l-2 2wf3-d 5qcw-1 4trz-2 5qcs-1 3dv5-3 3rsx-d 2q11-2 2bac-d 2bab-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

1oaoS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

E: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

F: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

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

1

A: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

hetero molecules

defined by author
48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	166.400, 166.400, 245.200
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
6	2	F

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	LEU	LEU	GLU	GLU	1	A	A	318 - 358	8 - 48
2	1	1	LEU	LEU	GLU	GLU	1	B	B	318 - 358	8 - 48
3	1	1	LEU	LEU	GLU	GLU	1	C	C	318 - 358	8 - 48
4	1	1	LEU	LEU	GLU	GLU	1	D	D	318 - 358	8 - 48
5	1	1	LEU	LEU	GLU	GLU	1	E	E	318 - 358	8 - 48
6	1	1	LEU	LEU	GLU	GLU	1	F	F	318 - 358	8 - 48
1	2	1	GLU	GLU	ILE	ILE	1	A	A	360 - 366	50 - 56
2	2	1	GLU	GLU	ILE	ILE	1	B	B	360 - 366	50 - 56
3	2	1	GLU	GLU	ILE	ILE	1	C	C	360 - 366	50 - 56
4	2	1	GLU	GLU	ILE	ILE	1	D	D	360 - 366	50 - 56
5	2	1	GLU	GLU	ILE	ILE	1	E	E	360 - 366	50 - 56
6	2	1	GLU	GLU	ILE	ILE	1	F	F	360 - 366	50 - 56
1	3	1	VAL	VAL	SER	SER	1	A	A	368 - 380	58 - 70
2	3	1	VAL	VAL	SER	SER	1	B	B	368 - 380	58 - 70
3	3	1	VAL	VAL	SER	SER	1	C	C	368 - 380	58 - 70
4	3	1	VAL	VAL	SER	SER	1	D	D	368 - 380	58 - 70
5	3	1	VAL	VAL	SER	SER	1	E	E	368 - 380	58 - 70
6	3	1	VAL	VAL	SER	SER	1	F	F	368 - 380	58 - 70
1	4	1	LEU	LEU	GLY	GLY	1	A	A	382 - 392	72 - 82
2	4	1	LEU	LEU	GLY	GLY	1	B	B	382 - 392	72 - 82
3	4	1	LEU	LEU	GLY	GLY	1	C	C	382 - 392	72 - 82
4	4	1	LEU	LEU	GLY	GLY	1	D	D	382 - 392	72 - 82
5	4	1	LEU	LEU	GLY	GLY	1	E	E	382 - 392	72 - 82
6	4	1	LEU	LEU	GLY	GLY	1	F	F	382 - 392	72 - 82
1	5	1	PHE	PHE	LYS	LYS	1	A	A	399 - 453	89 - 143
2	5	1	PHE	PHE	LYS	LYS	1	B	B	399 - 453	89 - 143
3	5	1	PHE	PHE	LYS	LYS	1	C	C	399 - 453	89 - 143
4	5	1	PHE	PHE	LYS	LYS	1	D	D	399 - 453	89 - 143
5	5	1	PHE	PHE	LYS	LYS	1	E	E	399 - 453	89 - 143
6	5	1	PHE	PHE	LYS	LYS	1	F	F	399 - 453	89 - 143
1	6	1	GLU	GLU	ALA	ALA	1	A	A	455 - 458	145 - 148
2	6	1	GLU	GLU	ALA	ALA	1	B	B	455 - 458	145 - 148
3	6	1	GLU	GLU	ALA	ALA	1	C	C	455 - 458	145 - 148
4	6	1	GLU	GLU	ALA	ALA	1	D	D	455 - 458	145 - 148
5	6	1	GLU	GLU	ALA	ALA	1	E	E	455 - 458	145 - 148
6	6	1	GLU	GLU	ALA	ALA	1	F	F	455 - 458	145 - 148
1	7	1	VAL	VAL	THR	THR	1	A	A	463 - 469	153 - 159
2	7	1	VAL	VAL	THR	THR	1	B	B	463 - 469	153 - 159
3	7	1	VAL	VAL	THR	THR	1	C	C	463 - 469	153 - 159
4	7	1	VAL	VAL	THR	THR	1	D	D	463 - 469	153 - 159
5	7	1	VAL	VAL	THR	THR	1	E	E	463 - 469	153 - 159
6	7	1	VAL	VAL	THR	THR	1	F	F	463 - 469	153 - 159
1	8	1	GLU	GLU	VAL	VAL	1	A	A	471 - 474	161 - 164
2	8	1	GLU	GLU	VAL	VAL	1	B	B	471 - 474	161 - 164
3	8	1	GLU	GLU	VAL	VAL	1	C	C	471 - 474	161 - 164
4	8	1	GLU	GLU	VAL	VAL	1	D	D	471 - 474	161 - 164
5	8	1	GLU	GLU	VAL	VAL	1	E	E	471 - 474	161 - 164
6	8	1	GLU	GLU	VAL	VAL	1	F	F	471 - 474	161 - 164
1	9	1	GLU	GLU	ARG	ARG	1	A	A	476 - 482	166 - 172
2	9	1	GLU	GLU	ARG	ARG	1	B	B	476 - 482	166 - 172
3	9	1	GLU	GLU	ARG	ARG	1	C	C	476 - 482	166 - 172
4	9	1	GLU	GLU	ARG	ARG	1	D	D	476 - 482	166 - 172
5	9	1	GLU	GLU	ARG	ARG	1	E	E	476 - 482	166 - 172
6	9	1	GLU	GLU	ARG	ARG	1	F	F	476 - 482	166 - 172
1	10	1	TYR	TYR	ASP	ASP	1	A	A	485 - 490	175 - 180
2	10	1	TYR	TYR	ASP	ASP	1	B	B	485 - 490	175 - 180
3	10	1	TYR	TYR	ASP	ASP	1	C	C	485 - 490	175 - 180
4	10	1	TYR	TYR	ASP	ASP	1	D	D	485 - 490	175 - 180
5	10	1	TYR	TYR	ASP	ASP	1	E	E	485 - 490	175 - 180
6	10	1	TYR	TYR	ASP	ASP	1	F	F	485 - 490	175 - 180
1	11	1	GLY	GLY	ASP	ASP	1	A	A	494 - 497	184 - 187
2	11	1	GLY	GLY	ASP	ASP	1	B	B	494 - 497	184 - 187
3	11	1	GLY	GLY	ASP	ASP	1	C	C	494 - 497	184 - 187
4	11	1	GLY	GLY	ASP	ASP	1	D	D	494 - 497	184 - 187
5	11	1	GLY	GLY	ASP	ASP	1	E	E	494 - 497	184 - 187
6	11	1	GLY	GLY	ASP	ASP	1	F	F	494 - 497	184 - 187
1	12	1	PHE	PHE	ALA	ALA	1	A	A	503 - 536	193 - 226
2	12	1	PHE	PHE	ALA	ALA	1	B	B	503 - 536	193 - 226
3	12	1	PHE	PHE	ALA	ALA	1	C	C	503 - 536	193 - 226
4	12	1	PHE	PHE	ALA	ALA	1	D	D	503 - 536	193 - 226
5	12	1	PHE	PHE	ALA	ALA	1	E	E	503 - 536	193 - 226
6	12	1	PHE	PHE	ALA	ALA	1	F	F	503 - 536	193 - 226
1	13	1	ALA	ALA	LYS	LYS	1	A	A	538 - 553	228 - 243
2	13	1	ALA	ALA	LYS	LYS	1	B	B	538 - 553	228 - 243
3	13	1	ALA	ALA	LYS	LYS	1	C	C	538 - 553	228 - 243
4	13	1	ALA	ALA	LYS	LYS	1	D	D	538 - 553	228 - 243
5	13	1	ALA	ALA	LYS	LYS	1	E	E	538 - 553	228 - 243
6	13	1	ALA	ALA	LYS	LYS	1	F	F	538 - 553	228 - 243
1	14	1	GLY	GLY	TRP	TRP	1	A	A	555 - 564	245 - 254
2	14	1	GLY	GLY	TRP	TRP	1	B	B	555 - 564	245 - 254
3	14	1	GLY	GLY	TRP	TRP	1	C	C	555 - 564	245 - 254
4	14	1	GLY	GLY	TRP	TRP	1	D	D	555 - 564	245 - 254
5	14	1	GLY	GLY	TRP	TRP	1	E	E	555 - 564	245 - 254
6	14	1	GLY	GLY	TRP	TRP	1	F	F	555 - 564	245 - 254
1	15	1	VAL	VAL	ASP	ASP	1	A	A	567 - 569	257 - 259
2	15	1	VAL	VAL	ASP	ASP	1	B	B	567 - 569	257 - 259
3	15	1	VAL	VAL	ASP	ASP	1	C	C	567 - 569	257 - 259
4	15	1	VAL	VAL	ASP	ASP	1	D	D	567 - 569	257 - 259
5	15	1	VAL	VAL	ASP	ASP	1	E	E	567 - 569	257 - 259
6	15	1	VAL	VAL	ASP	ASP	1	F	F	567 - 569	257 - 259
1	16	1	LEU	LEU	ASN	ASN	1	A	A	571 - 576	261 - 266
2	16	1	LEU	LEU	ASN	ASN	1	B	B	571 - 576	261 - 266
3	16	1	LEU	LEU	ASN	ASN	1	C	C	571 - 576	261 - 266
4	16	1	LEU	LEU	ASN	ASN	1	D	D	571 - 576	261 - 266
5	16	1	LEU	LEU	ASN	ASN	1	E	E	571 - 576	261 - 266
6	16	1	LEU	LEU	ASN	ASN	1	F	F	571 - 576	261 - 266
1	17	1	GLN	GLN	CYS	CYS	1	A	A	581 - 583	271 - 273
2	17	1	GLN	GLN	CYS	CYS	1	B	B	581 - 583	271 - 273
3	17	1	GLN	GLN	CYS	CYS	1	C	C	581 - 583	271 - 273
4	17	1	GLN	GLN	CYS	CYS	1	D	D	581 - 583	271 - 273
5	17	1	GLN	GLN	CYS	CYS	1	E	E	581 - 583	271 - 273
6	17	1	GLN	GLN	CYS	CYS	1	F	F	581 - 583	271 - 273
1	18	1	TYR	TYR	PRO	PRO	1	A	A	585 - 591	275 - 281
2	18	1	TYR	TYR	PRO	PRO	1	B	B	585 - 591	275 - 281
3	18	1	TYR	TYR	PRO	PRO	1	C	C	585 - 591	275 - 281
4	18	1	TYR	TYR	PRO	PRO	1	D	D	585 - 591	275 - 281
5	18	1	TYR	TYR	PRO	PRO	1	E	E	585 - 591	275 - 281
6	18	1	TYR	TYR	PRO	PRO	1	F	F	585 - 591	275 - 281
1	19	1	THR	THR	GLY	GLY	1	A	A	593 - 620	283 - 310
2	19	1	THR	THR	GLY	GLY	1	B	B	593 - 620	283 - 310
3	19	1	THR	THR	GLY	GLY	1	C	C	593 - 620	283 - 310
4	19	1	THR	THR	GLY	GLY	1	D	D	593 - 620	283 - 310
5	19	1	THR	THR	GLY	GLY	1	E	E	593 - 620	283 - 310
6	19	1	THR	THR	GLY	GLY	1	F	F	593 - 620	283 - 310
1	20	1	THR	THR	GLY	GLY	1	A	A	622 - 625	312 - 315
2	20	1	THR	THR	GLY	GLY	1	B	B	622 - 625	312 - 315
3	20	1	THR	THR	GLY	GLY	1	C	C	622 - 625	312 - 315
4	20	1	THR	THR	GLY	GLY	1	D	D	622 - 625	312 - 315
5	20	1	THR	THR	GLY	GLY	1	E	E	622 - 625	312 - 315
6	20	1	THR	THR	GLY	GLY	1	F	F	622 - 625	312 - 315
1	21	1	THR	THR	GLY	GLY	1	A	A	627 - 633	317 - 323
2	21	1	THR	THR	GLY	GLY	1	B	B	627 - 633	317 - 323
3	21	1	THR	THR	GLY	GLY	1	C	C	627 - 633	317 - 323
4	21	1	THR	THR	GLY	GLY	1	D	D	627 - 633	317 - 323
5	21	1	THR	THR	GLY	GLY	1	E	E	627 - 633	317 - 323
6	21	1	THR	THR	GLY	GLY	1	F	F	627 - 633	317 - 323
1	22	1	ILE	ILE	GLY	GLY	1	A	A	635 - 638	325 - 328
2	22	1	ILE	ILE	GLY	GLY	1	B	B	635 - 638	325 - 328
3	22	1	ILE	ILE	GLY	GLY	1	C	C	635 - 638	325 - 328
4	22	1	ILE	ILE	GLY	GLY	1	D	D	635 - 638	325 - 328
5	22	1	ILE	ILE	GLY	GLY	1	E	E	635 - 638	325 - 328
6	22	1	ILE	ILE	GLY	GLY	1	F	F	635 - 638	325 - 328
1	23	1	THR	THR	SER	SER	1	A	A	641 - 654	331 - 344
2	23	1	THR	THR	SER	SER	1	B	B	641 - 654	331 - 344
3	23	1	THR	THR	SER	SER	1	C	C	641 - 654	331 - 344
4	23	1	THR	THR	SER	SER	1	D	D	641 - 654	331 - 344
5	23	1	THR	THR	SER	SER	1	E	E	641 - 654	331 - 344
6	23	1	THR	THR	SER	SER	1	F	F	641 - 654	331 - 344
1	24	1	LYS	LYS	ARG	ARG	1	A	A	656 - 666	346 - 356
2	24	1	LYS	LYS	ARG	ARG	1	B	B	656 - 666	346 - 356
3	24	1	LYS	LYS	ARG	ARG	1	C	C	656 - 666	346 - 356
4	24	1	LYS	LYS	ARG	ARG	1	D	D	656 - 666	346 - 356
5	24	1	LYS	LYS	ARG	ARG	1	E	E	656 - 666	346 - 356
6	24	1	LYS	LYS	ARG	ARG	1	F	F	656 - 666	346 - 356
1	25	1	VAL	VAL	TRP	TRP	1	A	A	668 - 669	358 - 359
2	25	1	VAL	VAL	TRP	TRP	1	B	B	668 - 669	358 - 359
3	25	1	VAL	VAL	TRP	TRP	1	C	C	668 - 669	358 - 359
4	25	1	VAL	VAL	TRP	TRP	1	D	D	668 - 669	358 - 359
5	25	1	VAL	VAL	TRP	TRP	1	E	E	668 - 669	358 - 359
6	25	1	VAL	VAL	TRP	TRP	1	F	F	668 - 669	358 - 359
1	26	1	PRO	PRO	VAL	VAL	1	A	A	671 - 683	361 - 373
2	26	1	PRO	PRO	VAL	VAL	1	B	B	671 - 683	361 - 373
3	26	1	PRO	PRO	VAL	VAL	1	C	C	671 - 683	361 - 373
4	26	1	PRO	PRO	VAL	VAL	1	D	D	671 - 683	361 - 373
5	26	1	PRO	PRO	VAL	VAL	1	E	E	671 - 683	361 - 373
6	26	1	PRO	PRO	VAL	VAL	1	F	F	671 - 683	361 - 373
1	27	1	PHE	PHE	THR	THR	1	A	A	695 - 703	385 - 393
2	27	1	PHE	PHE	THR	THR	1	B	B	695 - 703	385 - 393
3	27	1	PHE	PHE	THR	THR	1	C	C	695 - 703	385 - 393
4	27	1	PHE	PHE	THR	THR	1	D	D	695 - 703	385 - 393
5	27	1	PHE	PHE	THR	THR	1	E	E	695 - 703	385 - 393
6	27	1	PHE	PHE	THR	THR	1	F	F	695 - 703	385 - 393
1	28	1	GLY	GLY	THR	THR	1	A	A	705 - 707	395 - 397
2	28	1	GLY	GLY	THR	THR	1	B	B	705 - 707	395 - 397
3	28	1	GLY	GLY	THR	THR	1	C	C	705 - 707	395 - 397
4	28	1	GLY	GLY	THR	THR	1	D	D	705 - 707	395 - 397
5	28	1	GLY	GLY	THR	THR	1	E	E	705 - 707	395 - 397
6	28	1	GLY	GLY	THR	THR	1	F	F	705 - 707	395 - 397
1	29	1	ASP	ASP	LEU	LEU	1	A	A	709 - 715	399 - 405
2	29	1	ASP	ASP	LEU	LEU	1	B	B	709 - 715	399 - 405
3	29	1	ASP	ASP	LEU	LEU	1	C	C	709 - 715	399 - 405
4	29	1	ASP	ASP	LEU	LEU	1	D	D	709 - 715	399 - 405
5	29	1	ASP	ASP	LEU	LEU	1	E	E	709 - 715	399 - 405
6	29	1	ASP	ASP	LEU	LEU	1	F	F	709 - 715	399 - 405
1	30	1	HIS	HIS	MET	MET	1	A	A	720 - 729	410 - 419
2	30	1	HIS	HIS	MET	MET	1	B	B	720 - 729	410 - 419
3	30	1	HIS	HIS	MET	MET	1	C	C	720 - 729	410 - 419
4	30	1	HIS	HIS	MET	MET	1	D	D	720 - 729	410 - 419
5	30	1	HIS	HIS	MET	MET	1	E	E	720 - 729	410 - 419
6	30	1	HIS	HIS	MET	MET	1	F	F	720 - 729	410 - 419
1	31	1	SF4	SF4	H2S	H2S	1	A	G - I	738 - 740
2	31	1	SF4	SF4	H2S	H2S	1	B	P - R	738 - 740
3	31	1	SF4	SF4	H2S	H2S	1	C	X - Z	738 - 740
4	31	1	SF4	SF4	H2S	H2S	1	D	GA - IA	738 - 740
5	31	1	SF4	SF4	H2S	H2S	1	E	NA - PA	738 - 740
6	31	1	SF4	SF4	H2S	H2S	1	F	VA - XA	738 - 740
1	1	2	ILE	ILE	LYS	LYS	3	A	A	316 - 317	6 - 7
2	1	2	ILE	ILE	LYS	LYS	3	B	B	316 - 317	6 - 7
3	1	2	ILE	ILE	LYS	LYS	3	C	C	316 - 317	6 - 7
4	1	2	ILE	ILE	LYS	LYS	3	D	D	316 - 317	6 - 7
5	1	2	ILE	ILE	LYS	LYS	3	E	E	316 - 317	6 - 7
6	1	2	ILE	ILE	LYS	LYS	3	F	F	316 - 317	6 - 7
1	2	2	SER	SER	SER	SER	3	A	A	359	49
2	2	2	SER	SER	SER	SER	3	B	B	359	49
3	2	2	SER	SER	SER	SER	3	C	C	359	49
4	2	2	SER	SER	SER	SER	3	D	D	359	49
5	2	2	SER	SER	SER	SER	3	E	E	359	49
6	2	2	SER	SER	SER	SER	3	F	F	359	49
1	3	2	GLU	GLU	GLU	GLU	3	A	A	367	57
2	3	2	GLU	GLU	GLU	GLU	3	B	B	367	57
3	3	2	GLU	GLU	GLU	GLU	3	C	C	367	57
4	3	2	GLU	GLU	GLU	GLU	3	D	D	367	57
5	3	2	GLU	GLU	GLU	GLU	3	E	E	367	57
6	3	2	GLU	GLU	GLU	GLU	3	F	F	367	57
1	4	2	LYS	LYS	LYS	LYS	3	A	A	381	71
2	4	2	LYS	LYS	LYS	LYS	3	B	B	381	71
3	4	2	LYS	LYS	LYS	LYS	3	C	C	381	71
4	4	2	LYS	LYS	LYS	LYS	3	D	D	381	71
5	4	2	LYS	LYS	LYS	LYS	3	E	E	381	71
6	4	2	LYS	LYS	LYS	LYS	3	F	F	381	71
1	5	2	ARG	ARG	ASP	ASP	3	A	A	393 - 398	83 - 88
2	5	2	ARG	ARG	ASP	ASP	3	B	B	393 - 398	83 - 88
3	5	2	ARG	ARG	ASP	ASP	3	C	C	393 - 398	83 - 88
4	5	2	ARG	ARG	ASP	ASP	3	D	D	393 - 398	83 - 88
5	5	2	ARG	ARG	ASP	ASP	3	E	E	393 - 398	83 - 88
6	5	2	ARG	ARG	ASP	ASP	3	F	F	393 - 398	83 - 88
1	6	2	GLU	GLU	GLU	GLU	3	A	A	454	144
2	6	2	GLU	GLU	GLU	GLU	3	B	B	454	144
3	6	2	GLU	GLU	GLU	GLU	3	C	C	454	144
4	6	2	GLU	GLU	GLU	GLU	3	D	D	454	144
5	6	2	GLU	GLU	GLU	GLU	3	E	E	454	144
6	6	2	GLU	GLU	GLU	GLU	3	F	F	454	144
1	7	2	ILE	ILE	ARG	ARG	3	A	A	459 - 462	149 - 152
2	7	2	ILE	ILE	ARG	ARG	3	B	B	459 - 462	149 - 152
3	7	2	ILE	ILE	ARG	ARG	3	C	C	459 - 462	149 - 152
4	7	2	ILE	ILE	ARG	ARG	3	D	D	459 - 462	149 - 152
5	7	2	ILE	ILE	ARG	ARG	3	E	E	459 - 462	149 - 152
6	7	2	ILE	ILE	ARG	ARG	3	F	F	459 - 462	149 - 152
1	8	2	ASP	ASP	ASP	ASP	3	A	A	470	160
2	8	2	ASP	ASP	ASP	ASP	3	B	B	470	160
3	8	2	ASP	ASP	ASP	ASP	3	C	C	470	160
4	8	2	ASP	ASP	ASP	ASP	3	D	D	470	160
5	8	2	ASP	ASP	ASP	ASP	3	E	E	470	160
6	8	2	ASP	ASP	ASP	ASP	3	F	F	470	160
1	9	2	LYS	LYS	LYS	LYS	3	A	A	475	165
2	9	2	LYS	LYS	LYS	LYS	3	B	B	475	165
3	9	2	LYS	LYS	LYS	LYS	3	C	C	475	165
4	9	2	LYS	LYS	LYS	LYS	3	D	D	475	165
5	9	2	LYS	LYS	LYS	LYS	3	E	E	475	165
6	9	2	LYS	LYS	LYS	LYS	3	F	F	475	165
1	10	2	GLU	GLU	LYS	LYS	3	A	A	483 - 484	173 - 174
2	10	2	GLU	GLU	LYS	LYS	3	B	B	483 - 484	173 - 174
3	10	2	GLU	GLU	LYS	LYS	3	C	C	483 - 484	173 - 174
4	10	2	GLU	GLU	LYS	LYS	3	D	D	483 - 484	173 - 174
5	10	2	GLU	GLU	LYS	LYS	3	E	E	483 - 484	173 - 174
6	10	2	GLU	GLU	LYS	LYS	3	F	F	483 - 484	173 - 174
1	11	2	ARG	ARG	ARG	ARG	3	A	A	491 - 493	181 - 183
2	11	2	ARG	ARG	ARG	ARG	3	B	B	491 - 493	181 - 183
3	11	2	ARG	ARG	ARG	ARG	3	C	C	491 - 493	181 - 183
4	11	2	ARG	ARG	ARG	ARG	3	D	D	491 - 493	181 - 183
5	11	2	ARG	ARG	ARG	ARG	3	E	E	491 - 493	181 - 183
6	11	2	ARG	ARG	ARG	ARG	3	F	F	491 - 493	181 - 183
1	12	2	GLU	GLU	THR	THR	3	A	A	498 - 502	188 - 192
2	12	2	GLU	GLU	THR	THR	3	B	B	498 - 502	188 - 192
3	12	2	GLU	GLU	THR	THR	3	C	C	498 - 502	188 - 192
4	12	2	GLU	GLU	THR	THR	3	D	D	498 - 502	188 - 192
5	12	2	GLU	GLU	THR	THR	3	E	E	498 - 502	188 - 192
6	12	2	GLU	GLU	THR	THR	3	F	F	498 - 502	188 - 192
1	13	2	LYS	LYS	LYS	LYS	3	A	A	537	227
2	13	2	LYS	LYS	LYS	LYS	3	B	B	537	227
3	13	2	LYS	LYS	LYS	LYS	3	C	C	537	227
4	13	2	LYS	LYS	LYS	LYS	3	D	D	537	227
5	13	2	LYS	LYS	LYS	LYS	3	E	E	537	227
6	13	2	LYS	LYS	LYS	LYS	3	F	F	537	227
1	14	2	GLU	GLU	GLU	GLU	3	A	A	554	244
2	14	2	GLU	GLU	GLU	GLU	3	B	B	554	244
3	14	2	GLU	GLU	GLU	GLU	3	C	C	554	244
4	14	2	GLU	GLU	GLU	GLU	3	D	D	554	244
5	14	2	GLU	GLU	GLU	GLU	3	E	E	554	244
6	14	2	GLU	GLU	GLU	GLU	3	F	F	554	244
1	15	2	LYS	LYS	SER	SER	3	A	A	565 - 566	255 - 256
2	15	2	LYS	LYS	SER	SER	3	B	B	565 - 566	255 - 256
3	15	2	LYS	LYS	SER	SER	3	C	C	565 - 566	255 - 256
4	15	2	LYS	LYS	SER	SER	3	D	D	565 - 566	255 - 256
5	15	2	LYS	LYS	SER	SER	3	E	E	565 - 566	255 - 256
6	15	2	LYS	LYS	SER	SER	3	F	F	565 - 566	255 - 256
1	16	2	TYR	TYR	TYR	TYR	3	A	A	570	260
2	16	2	TYR	TYR	TYR	TYR	3	B	B	570	260
3	16	2	TYR	TYR	TYR	TYR	3	C	C	570	260
4	16	2	TYR	TYR	TYR	TYR	3	D	D	570	260
5	16	2	TYR	TYR	TYR	TYR	3	E	E	570	260
6	16	2	TYR	TYR	TYR	TYR	3	F	F	570	260
1	17	2	ARG	ARG	GLU	GLU	3	A	A	577 - 580	267 - 270
2	17	2	ARG	ARG	GLU	GLU	3	B	B	577 - 580	267 - 270
3	17	2	ARG	ARG	GLU	GLU	3	C	C	577 - 580	267 - 270
4	17	2	ARG	ARG	GLU	GLU	3	D	D	577 - 580	267 - 270
5	17	2	ARG	ARG	GLU	GLU	3	E	E	577 - 580	267 - 270
6	17	2	ARG	ARG	GLU	GLU	3	F	F	577 - 580	267 - 270
1	18	2	LEU	LEU	LEU	LEU	3	A	A	584	274
2	18	2	LEU	LEU	LEU	LEU	3	B	B	584	274
3	18	2	LEU	LEU	LEU	LEU	3	C	C	584	274
4	18	2	LEU	LEU	LEU	LEU	3	D	D	584	274
5	18	2	LEU	LEU	LEU	LEU	3	E	E	584	274
6	18	2	LEU	LEU	LEU	LEU	3	F	F	584	274
1	19	2	MET	MET	MET	MET	3	A	A	592	282
2	19	2	MET	MET	MET	MET	3	B	B	592	282
3	19	2	MET	MET	MET	MET	3	C	C	592	282
4	19	2	MET	MET	MET	MET	3	D	D	592	282
5	19	2	MET	MET	MET	MET	3	E	E	592	282
6	19	2	MET	MET	MET	MET	3	F	F	592	282
1	20	2	MET	MET	MET	MET	3	A	A	621	311
2	20	2	MET	MET	MET	MET	3	B	B	621	311
3	20	2	MET	MET	MET	MET	3	C	C	621	311
4	20	2	MET	MET	MET	MET	3	D	D	621	311
5	20	2	MET	MET	MET	MET	3	E	E	621	311
6	20	2	MET	MET	MET	MET	3	F	F	621	311
1	21	2	MET	MET	MET	MET	3	A	A	626	316
2	21	2	MET	MET	MET	MET	3	B	B	626	316
3	21	2	MET	MET	MET	MET	3	C	C	626	316
4	21	2	MET	MET	MET	MET	3	D	D	626	316
5	21	2	MET	MET	MET	MET	3	E	E	626	316
6	21	2	MET	MET	MET	MET	3	F	F	626	316
1	22	2	MET	MET	MET	MET	3	A	A	634	324
2	22	2	MET	MET	MET	MET	3	B	B	634	324
3	22	2	MET	MET	MET	MET	3	C	C	634	324
4	22	2	MET	MET	MET	MET	3	D	D	634	324
5	22	2	MET	MET	MET	MET	3	E	E	634	324
6	22	2	MET	MET	MET	MET	3	F	F	634	324
1	23	2	THR	THR	THR	THR	3	A	A	639	329
2	23	2	THR	THR	THR	THR	3	B	B	639	329
3	23	2	THR	THR	THR	THR	3	C	C	639	329
4	23	2	THR	THR	THR	THR	3	D	D	639	329
5	23	2	THR	THR	THR	THR	3	E	E	639	329
6	23	2	THR	THR	THR	THR	3	F	F	639	329
1	24	2	LYS	LYS	LYS	LYS	3	A	A	655	345
2	24	2	LYS	LYS	LYS	LYS	3	B	B	655	345
3	24	2	LYS	LYS	LYS	LYS	3	C	C	655	345
4	24	2	LYS	LYS	LYS	LYS	3	D	D	655	345
5	24	2	LYS	LYS	LYS	LYS	3	E	E	655	345
6	24	2	LYS	LYS	LYS	LYS	3	F	F	655	345
1	25	2	ILE	ILE	ILE	ILE	3	A	A	667	357
2	25	2	ILE	ILE	ILE	ILE	3	B	B	667	357
3	25	2	ILE	ILE	ILE	ILE	3	C	C	667	357
4	25	2	ILE	ILE	ILE	ILE	3	D	D	667	357
5	25	2	ILE	ILE	ILE	ILE	3	E	E	667	357
6	25	2	ILE	ILE	ILE	ILE	3	F	F	667	357
1	26	2	MET	MET	MET	MET	3	A	A	670	360
2	26	2	MET	MET	MET	MET	3	B	B	670	360
3	26	2	MET	MET	MET	MET	3	C	C	670	360
4	26	2	MET	MET	MET	MET	3	D	D	670	360
5	26	2	MET	MET	MET	MET	3	E	E	670	360
6	26	2	MET	MET	MET	MET	3	F	F	670	360
1	27	2	ARG	ARG	ASP	ASP	3	A	A	684 - 694	374 - 384
2	27	2	ARG	ARG	ASP	ASP	3	B	B	684 - 694	374 - 384
3	27	2	ARG	ARG	ASP	ASP	3	C	C	684 - 694	374 - 384
4	27	2	ARG	ARG	ASP	ASP	3	D	D	684 - 694	374 - 384
5	27	2	ARG	ARG	ASP	ASP	3	E	E	684 - 694	374 - 384
6	27	2	ARG	ARG	ASP	ASP	3	F	F	684 - 694	374 - 384
1	28	2	ILE	ILE	ILE	ILE	3	A	A	704	394
2	28	2	ILE	ILE	ILE	ILE	3	B	B	704	394
3	28	2	ILE	ILE	ILE	ILE	3	C	C	704	394
4	28	2	ILE	ILE	ILE	ILE	3	D	D	704	394
5	28	2	ILE	ILE	ILE	ILE	3	E	E	704	394
6	28	2	ILE	ILE	ILE	ILE	3	F	F	704	394
1	29	2	VAL	VAL	VAL	VAL	3	A	A	708	398
2	29	2	VAL	VAL	VAL	VAL	3	B	B	708	398
3	29	2	VAL	VAL	VAL	VAL	3	C	C	708	398
4	29	2	VAL	VAL	VAL	VAL	3	D	D	708	398
5	29	2	VAL	VAL	VAL	VAL	3	E	E	708	398
6	29	2	VAL	VAL	VAL	VAL	3	F	F	708	398
1	30	2	GLU	GLU	ILE	ILE	3	A	A	716 - 728	406 - 418
2	30	2	GLU	GLU	ILE	ILE	3	B	B	716 - 728	406 - 418
3	30	2	GLU	GLU	ILE	ILE	3	C	C	716 - 728	406 - 418
4	30	2	GLU	GLU	ILE	ILE	3	D	D	716 - 728	406 - 418
5	30	2	GLU	GLU	ILE	ILE	3	E	E	716 - 728	406 - 418
6	30	2	GLU	GLU	ILE	ILE	3	F	F	716 - 728	406 - 418
1	31	2	ARG	ARG	ARG	ARG	3	A	A	730 - 735	420 - 425
2	31	2	ARG	ARG	ARG	ARG	3	B	B	730 - 735	420 - 425
3	31	2	ARG	ARG	ARG	ARG	3	C	C	730 - 735	420 - 425
4	31	2	ARG	ARG	ARG	ARG	3	D	D	730 - 735	420 - 425
5	31	2	ARG	ARG	ARG	ARG	3	E	E	730 - 735	420 - 425
6	31	2	ARG	ARG	ARG	ARG	3	F	F	730 - 735	420 - 425
1	32	2	SO4	SO4	SO4	SO4	3	A	J - N	741 - 745
2	32	2	SO4	SO4	SO4	SO4	3	D - B	FA - V	741 - 745
3	32	2	SO4	SO4	SO4	SO4	3	B - C	W - DA	741 - 745
4	32	2	SO4	SO4	SO4	SO4	3	C - D	EA - MA	741 - 745
5	32	2	SO4	SO4	SO4	SO4	3	F - E	UA - TA	741 - 745
6	32	2	SO4	SO4	SO4	SO4	3	A - F	J - BB	741 - 745

NCS ensembles :

ID
1
2

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / CODH/ACS / Acetyl-CoA synthase subunit / ACS subunit Mass: 47781.617 Da / Num. of mol.: 6 / Fragment: truncated domain, residues 311-729 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: acsB2 / Plasmid: pLHK07 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P27988, CO-methylating acetyl-CoA synthase

#1: Protein

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha / CODH/ACS / Acetyl-CoA synthase subunit / ACS subunit

Mass: 47781.617 Da / Num. of mol.: 6 / Fragment: truncated domain, residues 311-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Moorella thermoacetica (bacteria) / Gene: acsB2 / Plasmid: pLHK07 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase

-
Non-polymers , 6 types, 237 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H₂S
#5: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.42 Å³/Da / Density % sol: 64.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.008 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 12, 2004
Radiation	Monochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.008 Å / Relative weight: 1
Reflection	Resolution: 3→20 Å / Num. all: 78758 / Num. obs: 78342 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 51.823 Å² / R_merge(I) obs: 0.053 / Net I/σ(I): 19.6
Reflection shell	Resolution: 3→3.1 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.243 / Mean I/σ(I) obs: 6.3 / Num. measured obs: 55207 / Num. unique all: 7323 / Num. unique obs: 14222 / % possible all: 99.7

-
Phasing

Phasing	Method: molecular replacement
Phasing MR	Model details: Phaser MODE: MR_AUTO

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
Xnemo		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAO: ACS domain 2 (320-470) and domain 3 (500-729)

1oao

Resolution: 3→19.98 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.215 / WR_factor R_work: 0.179 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.88 / SU B: 28.231 / SU ML: 0.241 / SU R Cruickshank DPI: 0.289 / SU R_free: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: use of 12 TLS bodies and tight ncs restraints

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	3902	5 %	RANDOM
R_work	0.171	-	-	-
all	0.173	78758	-	-
obs	0.173	78314	99.47 %	-

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 max: 92.04 Å² / B_iso mean: 57.237 Å² / B_iso min: 20.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.83 Å²	-0.92 Å²	0 Å²
2-	-	-1.83 Å²	0 Å²
3-	-	-	2.75 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.33 Å	-
Luzzati d res low	-	3 Å
Luzzati sigma a	0.24 Å	-

Refinement step

Cycle: LAST / Resolution: 3→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19742	0	216	189	20147

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	20402
X-RAY DIFFRACTION	r_angle_refined_deg	1.586	2.009	27560
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.316	5	2522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.522	24.097	908
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.452	15	3546
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.873	15	138
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	2978
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15268
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	9395
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	13974
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	786
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.35	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.369	1.5	12798
X-RAY DIFFRACTION	r_mcangle_it	0.597	2	20254
X-RAY DIFFRACTION	r_scbond_it	1.07	3	8474
X-RAY DIFFRACTION	r_scangle_it	1.734	4.5	7233

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	2718	TIGHT POSITIONAL	0.1	0.1
1	2	B	2718	TIGHT POSITIONAL	0.09	0.1
1	3	C	2718	TIGHT POSITIONAL	0.1	0.1
1	4	D	2718	TIGHT POSITIONAL	0.1	0.1
1	5	E	2718	TIGHT POSITIONAL	0.09	0.1
1	6	F	2718	TIGHT POSITIONAL	0.1	0.1
1	1	A	2718	TIGHT THERMAL	0.38	1.5
1	2	B	2718	TIGHT THERMAL	0.36	1.5
1	3	C	2718	TIGHT THERMAL	0.35	1.5
1	4	D	2718	TIGHT THERMAL	0.42	1.5
1	5	E	2718	TIGHT THERMAL	0.41	1.5
1	6	F	2718	TIGHT THERMAL	0.35	1.5
2	1	A	308	TIGHT POSITIONAL	0.13	0.1
2	2	B	308	TIGHT POSITIONAL	0.12	0.1
2	3	C	308	TIGHT POSITIONAL	0.14	0.1
2	4	D	308	TIGHT POSITIONAL	0.1	0.1
2	5	E	308	TIGHT POSITIONAL	0.12	0.1
2	6	F	308	TIGHT POSITIONAL	0.12	0.1
2	1	A	346	LOOSE POSITIONAL	0.5	5
2	2	B	346	LOOSE POSITIONAL	0.54	5
2	3	C	346	LOOSE POSITIONAL	0.6	5
2	4	D	346	LOOSE POSITIONAL	0.49	5
2	5	E	346	LOOSE POSITIONAL	0.46	5
2	6	F	346	LOOSE POSITIONAL	0.49	5
2	1	A	308	TIGHT THERMAL	0.38	1.5
2	2	B	308	TIGHT THERMAL	0.29	1.5
2	3	C	308	TIGHT THERMAL	0.32	1.5
2	4	D	308	TIGHT THERMAL	0.36	1.5
2	5	E	308	TIGHT THERMAL	0.32	1.5
2	6	F	308	TIGHT THERMAL	0.31	1.5
2	1	A	346	LOOSE THERMAL	1.64	10
2	2	B	346	LOOSE THERMAL	2.11	10
2	3	C	346	LOOSE THERMAL	2.04	10
2	4	D	346	LOOSE THERMAL	2.06	10
2	5	E	346	LOOSE THERMAL	1.95	10
2	6	F	346	LOOSE THERMAL	1.95	10

LS refinement shell

Resolution: 3→3.076 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	285	-
R_work	0.248	5379	-
all	-	5664	-
obs	-	-	99.86 %

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	2.5164	-0.4767	0.5677	2.1299	-0.6421	1.2329	0.0311	-0.6292	0.1575	0.6938	-0.26	-0.392	-0.1897	0.178	0.2289	0.0417	-0.1005	-0.142	-0.0925	0.0114	-0.2502	104.9511	-5.2378	52.786
2	1.8827	0.6969	-0.6886	2.5446	-0.4996	1.7036	-0.2187	0.7833	-0.1509	-1.0721	0.1131	-0.2506	0.3874	-0.1009	0.1055	0.3351	0.0514	0.1271	0.0144	-0.0518	-0.3407	94.5496	-5.0734	-15.6336
3	1.3215	-0.061	-0.1326	1.6481	-1.2558	2.1617	0.0228	0.049	-0.2842	-0.3821	-0.5127	-0.8565	0.3386	0.5282	0.4899	-0.1076	0.2793	0.2471	-0.0953	0.3625	0.5237	132.078	-22.5985	19.0291
4	2.7233	0.0482	0.3076	1.7288	-0.3887	1.3216	0.0319	-0.1961	-0.4591	0.1254	-0.0948	0.1179	0.3632	-0.1248	0.0629	-0.1648	-0.0438	0.031	-0.372	-0.0419	-0.2807	79.4508	-27.4767	31.4016
5	2.1429	0.5277	-0.9321	1.8454	-0.5528	1.4716	0.1435	0.2853	0.5235	-0.1188	0.0067	0.4459	-0.2768	-0.301	-0.1502	-0.2083	0.1246	0.0132	-0.3154	-0.0057	-0.1679	74.2752	14.7212	12.5806
6	1.6658	-0.0441	0.1552	1.9864	-1.0753	1.8818	-0.0093	0.1155	0.1198	0.0373	-0.3829	-0.8928	-0.1265	0.5002	0.3922	-0.199	0.0229	0.1374	-0.1226	0.338	0.3098	128.3849	15.8335	8.6367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	317 - 737
2	X-RAY DIFFRACTION	1	A	738 - 745
3	X-RAY DIFFRACTION	2	B	317 - 736
4	X-RAY DIFFRACTION	2	B	738 - 745
5	X-RAY DIFFRACTION	3	C	317 - 736
6	X-RAY DIFFRACTION	3	C	738 - 745
7	X-RAY DIFFRACTION	4	D	317 - 737
8	X-RAY DIFFRACTION	4	D	738 - 745
9	X-RAY DIFFRACTION	5	E	317 - 736
10	X-RAY DIFFRACTION	5	E	738 - 745
11	X-RAY DIFFRACTION	6	F	317 - 736
12	X-RAY DIFFRACTION	6	F	738 - 745

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 6 types, 237 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 6 molecules ABCDEF

-Non-polymers , 6 types, 237 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 6 types, 237 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi