PDB-5cx7: Crystal Structure of PduOC:Heme Complex

ID or keywords:

Entry

Database: PDB / ID: 5cx7

Title

Crystal Structure of PduOC:Heme Complex

Components

ATP:cob(I)alamin adenosyltransferase

Keywords

UNKNOWN FUNCTION / Bis-His / Heme binding domain / PduOC

Function / homology

Function and homology information

propanediol degradation polyhedral organelle / propanediol catabolic process / corrinoid adenosyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin biosynthetic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Livingstone (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Geremia, S. / Hickey, N. / Ortiz de Orue Lucana, D.

Citation

Journal: Front Microbiol / Year: 2016
Title: The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode.
Authors: Ortiz de Orue Lucana, D. / Hickey, N. / Hensel, M. / Klare, J.P. / Geremia, S. / Tiufiakova, T. / Torda, A.E.

History

Deposition	Jul 28, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2016	Group: Database references
Revision 1.2	Nov 23, 2016	Group: Derived calculations
Revision 1.3	Jan 10, 2024	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 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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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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Download

PDBx/mmCIF format	5cx7.cif.gz	461.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5cx7.ent.gz	375.7 KB	Display	PDB format
PDBx/mmJSON format	5cx7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cx7_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	5cx7_full_validation.pdf.gz	3.1 MB	Display
Data in XML	5cx7_validation.xml.gz	103 KB	Display
Data in CIF	5cx7_validation.cif.gz	137.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cx/5cx7 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cx7	HTTPS FTP

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Related structure data

Related structure data	2a2lS S: Starting model for refinement
Similar structure data	3dc5-1 6qzn-1 4rvc-1 5xyo-1 2e6e-d 6elk-1 5xyt-1 2a2l-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ATP:cob(I)alamin adenosyltransferase

B: ATP:cob(I)alamin adenosyltransferase

C: ATP:cob(I)alamin adenosyltransferase

D: ATP:cob(I)alamin adenosyltransferase

E: ATP:cob(I)alamin adenosyltransferase

F: ATP:cob(I)alamin adenosyltransferase

G: ATP:cob(I)alamin adenosyltransferase

H: ATP:cob(I)alamin adenosyltransferase

I: ATP:cob(I)alamin adenosyltransferase

J: ATP:cob(I)alamin adenosyltransferase

K: ATP:cob(I)alamin adenosyltransferase

L: ATP:cob(I)alamin adenosyltransferase

M: ATP:cob(I)alamin adenosyltransferase

N: ATP:cob(I)alamin adenosyltransferase

O: ATP:cob(I)alamin adenosyltransferase

P: ATP:cob(I)alamin adenosyltransferase

hetero molecules

255 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP:cob(I)alamin adenosyltransferase

B: ATP:cob(I)alamin adenosyltransferase

C: ATP:cob(I)alamin adenosyltransferase

D: ATP:cob(I)alamin adenosyltransferase

E: ATP:cob(I)alamin adenosyltransferase

F: ATP:cob(I)alamin adenosyltransferase

G: ATP:cob(I)alamin adenosyltransferase

H: ATP:cob(I)alamin adenosyltransferase

hetero molecules

defined by author&software
127 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: ATP:cob(I)alamin adenosyltransferase

J: ATP:cob(I)alamin adenosyltransferase

K: ATP:cob(I)alamin adenosyltransferase

L: ATP:cob(I)alamin adenosyltransferase

M: ATP:cob(I)alamin adenosyltransferase

N: ATP:cob(I)alamin adenosyltransferase

O: ATP:cob(I)alamin adenosyltransferase

P: ATP:cob(I)alamin adenosyltransferase

hetero molecules

defined by author&software
127 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.300, 130.120, 120.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	A	A	10 - 147	10 - 147
2	1	GLN	GLN	B	B	10 - 147	10 - 147
1	2	GLN	GLN	A	A	10 - 147	10 - 147
2	2	GLN	GLN	C	C	10 - 147	10 - 147
1	3	GLN	GLN	A	A	10 - 147	10 - 147
2	3	GLN	GLN	D	D	10 - 147	10 - 147
1	4	HIS	HIS	A	A	10 - 146	10 - 146
2	4	HIS	HIS	E	E	10 - 146	10 - 146
1	5	GLN	GLN	A	A	10 - 147	10 - 147
2	5	GLN	GLN	F	F	10 - 147	10 - 147
1	6	GLN	GLN	A	A	10 - 147	10 - 147
2	6	GLN	GLN	G	G	10 - 147	10 - 147
1	7	GLN	GLN	A	A	10 - 147	10 - 147
2	7	GLN	GLN	H	H	10 - 147	10 - 147
1	8	GLN	GLN	A	A	10 - 147	10 - 147
2	8	GLN	GLN	I	I	10 - 147	10 - 147
1	9	GLN	GLN	A	A	10 - 147	10 - 147
2	9	GLN	GLN	J	J	10 - 147	10 - 147
1	10	GLN	GLN	A	A	10 - 147	10 - 147
2	10	GLN	GLN	K	K	10 - 147	10 - 147
1	11	GLN	GLN	A	A	10 - 147	10 - 147
2	11	GLN	GLN	L	L	10 - 147	10 - 147
1	12	GLN	GLN	A	A	10 - 147	10 - 147
2	12	GLN	GLN	M	M	10 - 147	10 - 147
1	13	GLN	GLN	A	A	10 - 147	10 - 147
2	13	GLN	GLN	N	N	10 - 147	10 - 147
1	14	GLN	GLN	A	A	10 - 147	10 - 147
2	14	GLN	GLN	O	O	10 - 147	10 - 147
1	15	GLN	GLN	A	A	10 - 147	10 - 147
2	15	GLN	GLN	P	P	10 - 147	10 - 147
1	16	GLN	GLN	B	B	10 - 147	10 - 147
2	16	GLN	GLN	C	C	10 - 147	10 - 147
1	17	GLN	GLN	B	B	10 - 147	10 - 147
2	17	GLN	GLN	D	D	10 - 147	10 - 147
1	18	HIS	HIS	B	B	10 - 146	10 - 146
2	18	HIS	HIS	E	E	10 - 146	10 - 146
1	19	GLN	GLN	B	B	10 - 147	10 - 147
2	19	GLN	GLN	F	F	10 - 147	10 - 147
1	20	GLN	GLN	B	B	10 - 147	10 - 147
2	20	GLN	GLN	G	G	10 - 147	10 - 147
1	21	GLN	GLN	B	B	10 - 147	10 - 147
2	21	GLN	GLN	H	H	10 - 147	10 - 147
1	22	GLN	GLN	B	B	10 - 147	10 - 147
2	22	GLN	GLN	I	I	10 - 147	10 - 147
1	23	GLN	GLN	B	B	10 - 147	10 - 147
2	23	GLN	GLN	J	J	10 - 147	10 - 147
1	24	GLN	GLN	B	B	10 - 147	10 - 147
2	24	GLN	GLN	K	K	10 - 147	10 - 147
1	25	GLN	GLN	B	B	10 - 147	10 - 147
2	25	GLN	GLN	L	L	10 - 147	10 - 147
1	26	GLN	GLN	B	B	10 - 147	10 - 147
2	26	GLN	GLN	M	M	10 - 147	10 - 147
1	27	GLN	GLN	B	B	10 - 147	10 - 147
2	27	GLN	GLN	N	N	10 - 147	10 - 147
1	28	GLN	GLN	B	B	10 - 147	10 - 147
2	28	GLN	GLN	O	O	10 - 147	10 - 147
1	29	GLN	GLN	B	B	10 - 147	10 - 147
2	29	GLN	GLN	P	P	10 - 147	10 - 147
1	30	GLN	GLN	C	C	10 - 147	10 - 147
2	30	GLN	GLN	D	D	10 - 147	10 - 147
1	31	HIS	HIS	C	C	10 - 146	10 - 146
2	31	HIS	HIS	E	E	10 - 146	10 - 146
1	32	GLN	GLN	C	C	10 - 147	10 - 147
2	32	GLN	GLN	F	F	10 - 147	10 - 147
1	33	GLN	GLN	C	C	10 - 147	10 - 147
2	33	GLN	GLN	G	G	10 - 147	10 - 147
1	34	GLN	GLN	C	C	10 - 147	10 - 147
2	34	GLN	GLN	H	H	10 - 147	10 - 147
1	35	GLN	GLN	C	C	10 - 147	10 - 147
2	35	GLN	GLN	I	I	10 - 147	10 - 147
1	36	GLN	GLN	C	C	10 - 147	10 - 147
2	36	GLN	GLN	J	J	10 - 147	10 - 147
1	37	GLN	GLN	C	C	10 - 147	10 - 147
2	37	GLN	GLN	K	K	10 - 147	10 - 147
1	38	GLN	GLN	C	C	10 - 147	10 - 147
2	38	GLN	GLN	L	L	10 - 147	10 - 147
1	39	GLN	GLN	C	C	10 - 147	10 - 147
2	39	GLN	GLN	M	M	10 - 147	10 - 147
1	40	GLN	GLN	C	C	10 - 147	10 - 147
2	40	GLN	GLN	N	N	10 - 147	10 - 147
1	41	GLN	GLN	C	C	10 - 147	10 - 147
2	41	GLN	GLN	O	O	10 - 147	10 - 147
1	42	GLN	GLN	C	C	10 - 147	10 - 147
2	42	GLN	GLN	P	P	10 - 147	10 - 147
1	43	HIS	HIS	D	D	10 - 146	10 - 146
2	43	HIS	HIS	E	E	10 - 146	10 - 146
1	44	GLN	GLN	D	D	10 - 147	10 - 147
2	44	GLN	GLN	F	F	10 - 147	10 - 147
1	45	GLN	GLN	D	D	10 - 147	10 - 147
2	45	GLN	GLN	G	G	10 - 147	10 - 147
1	46	GLN	GLN	D	D	10 - 147	10 - 147
2	46	GLN	GLN	H	H	10 - 147	10 - 147
1	47	GLN	GLN	D	D	10 - 147	10 - 147
2	47	GLN	GLN	I	I	10 - 147	10 - 147
1	48	GLN	GLN	D	D	10 - 147	10 - 147
2	48	GLN	GLN	J	J	10 - 147	10 - 147
1	49	GLN	GLN	D	D	10 - 147	10 - 147
2	49	GLN	GLN	K	K	10 - 147	10 - 147
1	50	GLN	GLN	D	D	10 - 147	10 - 147
2	50	GLN	GLN	L	L	10 - 147	10 - 147
1	51	GLN	GLN	D	D	10 - 147	10 - 147
2	51	GLN	GLN	M	M	10 - 147	10 - 147
1	52	GLN	GLN	D	D	10 - 147	10 - 147
2	52	GLN	GLN	N	N	10 - 147	10 - 147
1	53	GLN	GLN	D	D	10 - 147	10 - 147
2	53	GLN	GLN	O	O	10 - 147	10 - 147
1	54	GLN	GLN	D	D	10 - 147	10 - 147
2	54	GLN	GLN	P	P	10 - 147	10 - 147
1	55	HIS	HIS	E	E	10 - 146	10 - 146
2	55	HIS	HIS	F	F	10 - 146	10 - 146
1	56	HIS	HIS	E	E	10 - 146	10 - 146
2	56	HIS	HIS	G	G	10 - 146	10 - 146
1	57	HIS	HIS	E	E	10 - 146	10 - 146
2	57	HIS	HIS	H	H	10 - 146	10 - 146
1	58	HIS	HIS	E	E	10 - 146	10 - 146
2	58	HIS	HIS	I	I	10 - 146	10 - 146
1	59	HIS	HIS	E	E	10 - 146	10 - 146
2	59	HIS	HIS	J	J	10 - 146	10 - 146
1	60	HIS	HIS	E	E	10 - 146	10 - 146
2	60	HIS	HIS	K	K	10 - 146	10 - 146
1	61	HIS	HIS	E	E	10 - 146	10 - 146
2	61	HIS	HIS	L	L	10 - 146	10 - 146
1	62	HIS	HIS	E	E	10 - 146	10 - 146
2	62	HIS	HIS	M	M	10 - 146	10 - 146
1	63	HIS	HIS	E	E	10 - 146	10 - 146
2	63	HIS	HIS	N	N	10 - 146	10 - 146
1	64	HIS	HIS	E	E	10 - 146	10 - 146
2	64	HIS	HIS	O	O	10 - 146	10 - 146
1	65	HIS	HIS	E	E	10 - 146	10 - 146
2	65	HIS	HIS	P	P	10 - 146	10 - 146
1	66	GLN	GLN	F	F	10 - 147	10 - 147
2	66	GLN	GLN	G	G	10 - 147	10 - 147
1	67	GLN	GLN	F	F	10 - 147	10 - 147
2	67	GLN	GLN	H	H	10 - 147	10 - 147
1	68	GLN	GLN	F	F	10 - 147	10 - 147
2	68	GLN	GLN	I	I	10 - 147	10 - 147
1	69	GLN	GLN	F	F	10 - 147	10 - 147
2	69	GLN	GLN	J	J	10 - 147	10 - 147
1	70	GLN	GLN	F	F	10 - 147	10 - 147
2	70	GLN	GLN	K	K	10 - 147	10 - 147
1	71	GLN	GLN	F	F	10 - 147	10 - 147
2	71	GLN	GLN	L	L	10 - 147	10 - 147
1	72	GLN	GLN	F	F	10 - 147	10 - 147
2	72	GLN	GLN	M	M	10 - 147	10 - 147
1	73	GLN	GLN	F	F	10 - 147	10 - 147
2	73	GLN	GLN	N	N	10 - 147	10 - 147
1	74	GLN	GLN	F	F	10 - 147	10 - 147
2	74	GLN	GLN	O	O	10 - 147	10 - 147
1	75	GLN	GLN	F	F	10 - 147	10 - 147
2	75	GLN	GLN	P	P	10 - 147	10 - 147
1	76	GLN	GLN	G	G	10 - 147	10 - 147
2	76	GLN	GLN	H	H	10 - 147	10 - 147
1	77	GLN	GLN	G	G	10 - 147	10 - 147
2	77	GLN	GLN	I	I	10 - 147	10 - 147
1	78	GLN	GLN	G	G	10 - 147	10 - 147
2	78	GLN	GLN	J	J	10 - 147	10 - 147
1	79	GLN	GLN	G	G	10 - 147	10 - 147
2	79	GLN	GLN	K	K	10 - 147	10 - 147
1	80	GLN	GLN	G	G	10 - 147	10 - 147
2	80	GLN	GLN	L	L	10 - 147	10 - 147
1	81	GLN	GLN	G	G	10 - 147	10 - 147
2	81	GLN	GLN	M	M	10 - 147	10 - 147
1	82	GLN	GLN	G	G	10 - 147	10 - 147
2	82	GLN	GLN	N	N	10 - 147	10 - 147
1	83	GLN	GLN	G	G	10 - 147	10 - 147
2	83	GLN	GLN	O	O	10 - 147	10 - 147
1	84	GLN	GLN	G	G	10 - 147	10 - 147
2	84	GLN	GLN	P	P	10 - 147	10 - 147
1	85	GLN	GLN	H	H	10 - 147	10 - 147
2	85	GLN	GLN	I	I	10 - 147	10 - 147
1	86	GLN	GLN	H	H	10 - 147	10 - 147
2	86	GLN	GLN	J	J	10 - 147	10 - 147
1	87	GLN	GLN	H	H	10 - 147	10 - 147
2	87	GLN	GLN	K	K	10 - 147	10 - 147
1	88	GLN	GLN	H	H	10 - 147	10 - 147
2	88	GLN	GLN	L	L	10 - 147	10 - 147
1	89	GLN	GLN	H	H	10 - 147	10 - 147
2	89	GLN	GLN	M	M	10 - 147	10 - 147
1	90	GLN	GLN	H	H	10 - 147	10 - 147
2	90	GLN	GLN	N	N	10 - 147	10 - 147
1	91	GLN	GLN	H	H	10 - 147	10 - 147
2	91	GLN	GLN	O	O	10 - 147	10 - 147
1	92	GLN	GLN	H	H	10 - 147	10 - 147
2	92	GLN	GLN	P	P	10 - 147	10 - 147
1	93	GLN	GLN	I	I	10 - 147	10 - 147
2	93	GLN	GLN	J	J	10 - 147	10 - 147
1	94	GLN	GLN	I	I	10 - 147	10 - 147
2	94	GLN	GLN	K	K	10 - 147	10 - 147
1	95	GLN	GLN	I	I	10 - 147	10 - 147
2	95	GLN	GLN	L	L	10 - 147	10 - 147
1	96	GLN	GLN	I	I	10 - 147	10 - 147
2	96	GLN	GLN	M	M	10 - 147	10 - 147
1	97	GLN	GLN	I	I	10 - 147	10 - 147
2	97	GLN	GLN	N	N	10 - 147	10 - 147
1	98	GLN	GLN	I	I	10 - 147	10 - 147
2	98	GLN	GLN	O	O	10 - 147	10 - 147
1	99	GLN	GLN	I	I	10 - 147	10 - 147
2	99	GLN	GLN	P	P	10 - 147	10 - 147
1	100	GLN	GLN	J	J	10 - 147	10 - 147
2	100	GLN	GLN	K	K	10 - 147	10 - 147
1	101	GLN	GLN	J	J	10 - 147	10 - 147
2	101	GLN	GLN	L	L	10 - 147	10 - 147
1	102	GLN	GLN	J	J	10 - 147	10 - 147
2	102	GLN	GLN	M	M	10 - 147	10 - 147
1	103	GLN	GLN	J	J	10 - 147	10 - 147
2	103	GLN	GLN	N	N	10 - 147	10 - 147
1	104	GLN	GLN	J	J	10 - 147	10 - 147
2	104	GLN	GLN	O	O	10 - 147	10 - 147
1	105	GLN	GLN	J	J	10 - 147	10 - 147
2	105	GLN	GLN	P	P	10 - 147	10 - 147
1	106	GLN	GLN	K	K	10 - 147	10 - 147
2	106	GLN	GLN	L	L	10 - 147	10 - 147
1	107	GLN	GLN	K	K	10 - 147	10 - 147
2	107	GLN	GLN	M	M	10 - 147	10 - 147
1	108	GLN	GLN	K	K	10 - 147	10 - 147
2	108	GLN	GLN	N	N	10 - 147	10 - 147
1	109	GLN	GLN	K	K	10 - 147	10 - 147
2	109	GLN	GLN	O	O	10 - 147	10 - 147
1	110	GLN	GLN	K	K	10 - 147	10 - 147
2	110	GLN	GLN	P	P	10 - 147	10 - 147
1	111	GLN	GLN	L	L	10 - 147	10 - 147
2	111	GLN	GLN	M	M	10 - 147	10 - 147
1	112	GLN	GLN	L	L	10 - 147	10 - 147
2	112	GLN	GLN	N	N	10 - 147	10 - 147
1	113	GLN	GLN	L	L	10 - 147	10 - 147
2	113	GLN	GLN	O	O	10 - 147	10 - 147
1	114	GLN	GLN	L	L	10 - 147	10 - 147
2	114	GLN	GLN	P	P	10 - 147	10 - 147
1	115	GLN	GLN	M	M	10 - 147	10 - 147
2	115	GLN	GLN	N	N	10 - 147	10 - 147
1	116	GLN	GLN	M	M	10 - 147	10 - 147
2	116	GLN	GLN	O	O	10 - 147	10 - 147
1	117	GLN	GLN	M	M	10 - 147	10 - 147
2	117	GLN	GLN	P	P	10 - 147	10 - 147
1	118	GLN	GLN	N	N	10 - 147	10 - 147
2	118	GLN	GLN	O	O	10 - 147	10 - 147
1	119	GLN	GLN	N	N	10 - 147	10 - 147
2	119	GLN	GLN	P	P	10 - 147	10 - 147
1	120	GLN	GLN	O	O	10 - 147	10 - 147
2	120	GLN	GLN	P	P	10 - 147	10 - 147

NCS ensembles :

-
Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein	ATP:cob(I)alamin adenosyltransferase Mass: 15437.539 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Livingstone (bacteria) Gene: VN13_17650 / Plasmid: pETPduO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F0IPG3, UniProt: A0A1A9TAI7*PLUS

#1: Protein

ATP:cob(I)alamin adenosyltransferase

Mass: 15437.539 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Livingstone (bacteria)
Gene: VN13_17650 / Plasmid: pETPduO / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F0IPG3, UniProt: A0A1A9TAI7*PLUS

-
Non-polymers , 6 types, 1498 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1441 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.76 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350 15% (w/v), 0.1 M magnesium formate

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ELETTRA

/ Beamline: 5.2R / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2015

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.204
1	1	-h,-k,l	2	0.796

Reflection

Resolution: 1.97→33.07 Å / Num. obs: 152372 / % possible obs: 98.2 % / Redundancy: 2.64 % / R_merge(I) obs: 0.091 / Net I/σ(I): 7.8

Reflection shell

Resolution: 1.97→2.08 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Num. unique all: 22309 / % possible all: 98.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2A2L

2a2l

Resolution: 1.97→33.07 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.258 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18564	7771	5.1 %	RANDOM
R_work	0.15803	-	-	-
obs	0.15943	144524	97.98 %	-

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: 22.703 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.87 Å²	-0 Å²	1.52 Å²
2-	-	18.86 Å²	0 Å²
3-	-	-	-11 Å²

Refinement step

Cycle: 1 / Resolution: 1.97→33.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16391	0	518	1441	18350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	17237
X-RAY DIFFRACTION	r_bond_other_d	0.016	0.02	16605
X-RAY DIFFRACTION	r_angle_refined_deg	1.998	1.98	23656
X-RAY DIFFRACTION	r_angle_other_deg	2.196	3	37967
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.861	5	2193
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.253	24.75	640
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.033	15	2624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.957	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	2778
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	19751
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	3841
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	2.16	1.983	8820
X-RAY DIFFRACTION	r_mcbond_other	2.16	1.983	8819
X-RAY DIFFRACTION	r_mcangle_it	2.926	2.963	10997
X-RAY DIFFRACTION	r_mcangle_other	2.926	2.963	10998
X-RAY DIFFRACTION	r_scbond_it	3.241	2.442	8417
X-RAY DIFFRACTION	r_scbond_other	3.241	2.442	8417
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.741	3.554	12660
X-RAY DIFFRACTION	r_long_range_B_refined	6.879	18.395	20891
X-RAY DIFFRACTION	r_long_range_B_other	6.88	18.379	20880
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	16460	0.07
1	2	B	16460	0.07
2	1	A	16544	0.07
2	2	C	16544	0.07
3	1	A	16610	0.07
3	2	D	16610	0.07
4	1	A	16400	0.07
4	2	E	16400	0.07
5	1	A	16520	0.07
5	2	F	16520	0.07
6	1	A	16512	0.07
6	2	G	16512	0.07
7	1	A	16582	0.07
7	2	H	16582	0.07
8	1	A	16480	0.07
8	2	I	16480	0.07
9	1	A	16468	0.08
9	2	J	16468	0.08
10	1	A	16644	0.06
10	2	K	16644	0.06
11	1	A	16600	0.07
11	2	L	16600	0.07
12	1	A	16382	0.08
12	2	M	16382	0.08
13	1	A	16422	0.08
13	2	N	16422	0.08
14	1	A	16594	0.07
14	2	O	16594	0.07
15	1	A	16380	0.08
15	2	P	16380	0.08
16	1	B	16750	0.07
16	2	C	16750	0.07
17	1	B	16618	0.07
17	2	D	16618	0.07
18	1	B	16374	0.08
18	2	E	16374	0.08
19	1	B	16790	0.07
19	2	F	16790	0.07
20	1	B	16822	0.06
20	2	G	16822	0.06
21	1	B	16756	0.06
21	2	H	16756	0.06
22	1	B	16858	0.05
22	2	I	16858	0.05
23	1	B	16972	0.04
23	2	J	16972	0.04
24	1	B	16676	0.07
24	2	K	16676	0.07
25	1	B	16714	0.07
25	2	L	16714	0.07
26	1	B	16970	0.04
26	2	M	16970	0.04
27	1	B	16904	0.06
27	2	N	16904	0.06
28	1	B	16748	0.06
28	2	O	16748	0.06
29	1	B	16748	0.06
29	2	P	16748	0.06
30	1	C	16642	0.07
30	2	D	16642	0.07
31	1	C	16414	0.07
31	2	E	16414	0.07
32	1	C	16550	0.08
32	2	F	16550	0.08
33	1	C	16550	0.08
33	2	G	16550	0.08
34	1	C	16582	0.08
34	2	H	16582	0.08
35	1	C	16676	0.07
35	2	I	16676	0.07
36	1	C	16774	0.07
36	2	J	16774	0.07
37	1	C	16818	0.05
37	2	K	16818	0.05
38	1	C	16634	0.07
38	2	L	16634	0.07
39	1	C	16734	0.07
39	2	M	16734	0.07
40	1	C	16728	0.07
40	2	N	16728	0.07
41	1	C	16608	0.07
41	2	O	16608	0.07
42	1	C	16672	0.07
42	2	P	16672	0.07
43	1	D	16720	0.06
43	2	E	16720	0.06
44	1	D	16798	0.06
44	2	F	16798	0.06
45	1	D	16776	0.06
45	2	G	16776	0.06
46	1	D	16732	0.07
46	2	H	16732	0.07
47	1	D	16730	0.07
47	2	I	16730	0.07
48	1	D	16676	0.07
48	2	J	16676	0.07
49	1	D	16738	0.06
49	2	K	16738	0.06
50	1	D	16934	0.05
50	2	L	16934	0.05
51	1	D	16704	0.07
51	2	M	16704	0.07
52	1	D	16676	0.07
52	2	N	16676	0.07
53	1	D	16850	0.06
53	2	O	16850	0.06
54	1	D	16610	0.08
54	2	P	16610	0.08
55	1	E	16544	0.06
55	2	F	16544	0.06
56	1	E	16534	0.07
56	2	G	16534	0.07
57	1	E	16548	0.07
57	2	H	16548	0.07
58	1	E	16490	0.08
58	2	I	16490	0.08
59	1	E	16416	0.07
59	2	J	16416	0.07
60	1	E	16508	0.06
60	2	K	16508	0.06
61	1	E	16652	0.06
61	2	L	16652	0.06
62	1	E	16444	0.08
62	2	M	16444	0.08
63	1	E	16426	0.08
63	2	N	16426	0.08
64	1	E	16596	0.07
64	2	O	16596	0.07
65	1	E	16422	0.08
65	2	P	16422	0.08
66	1	F	16960	0.05
66	2	G	16960	0.05
67	1	F	16790	0.07
67	2	H	16790	0.07
68	1	F	16762	0.07
68	2	I	16762	0.07
69	1	F	16788	0.06
69	2	J	16788	0.06
70	1	F	16748	0.06
70	2	K	16748	0.06
71	1	F	16922	0.05
71	2	L	16922	0.05
72	1	F	16848	0.06
72	2	M	16848	0.06
73	1	F	16818	0.06
73	2	N	16818	0.06
74	1	F	16920	0.05
74	2	O	16920	0.05
75	1	F	16596	0.07
75	2	P	16596	0.07
76	1	G	16812	0.06
76	2	H	16812	0.06
77	1	G	16736	0.07
77	2	I	16736	0.07
78	1	G	16870	0.05
78	2	J	16870	0.05
79	1	G	16756	0.06
79	2	K	16756	0.06
80	1	G	16918	0.05
80	2	L	16918	0.05
81	1	G	16888	0.06
81	2	M	16888	0.06
82	1	G	16752	0.07
82	2	N	16752	0.07
83	1	G	16978	0.04
83	2	O	16978	0.04
84	1	G	16618	0.07
84	2	P	16618	0.07
85	1	H	16578	0.08
85	2	I	16578	0.08
86	1	H	16652	0.07
86	2	J	16652	0.07
87	1	H	16684	0.07
87	2	K	16684	0.07
88	1	H	16836	0.07
88	2	L	16836	0.07
89	1	H	16640	0.07
89	2	M	16640	0.07
90	1	H	16578	0.08
90	2	N	16578	0.08
91	1	H	16950	0.06
91	2	O	16950	0.06
92	1	H	16824	0.05
92	2	P	16824	0.05
93	1	I	16898	0.05
93	2	J	16898	0.05
94	1	I	16612	0.07
94	2	K	16612	0.07
95	1	I	16708	0.07
95	2	L	16708	0.07
96	1	I	16940	0.06
96	2	M	16940	0.06
97	1	I	16852	0.07
97	2	N	16852	0.07
98	1	I	16700	0.07
98	2	O	16700	0.07
99	1	I	16706	0.07
99	2	P	16706	0.07
100	1	J	16706	0.07
100	2	K	16706	0.07
101	1	J	16722	0.06
101	2	L	16722	0.06
102	1	J	16980	0.04
102	2	M	16980	0.04
103	1	J	16910	0.05
103	2	N	16910	0.05
104	1	J	16758	0.06
104	2	O	16758	0.06
105	1	J	16756	0.06
105	2	P	16756	0.06
106	1	K	16742	0.06
106	2	L	16742	0.06
107	1	K	16630	0.07
107	2	M	16630	0.07
108	1	K	16646	0.07
108	2	N	16646	0.07
109	1	K	16722	0.07
109	2	O	16722	0.07
110	1	K	16482	0.08
110	2	P	16482	0.08
111	1	L	16796	0.07
111	2	M	16796	0.07
112	1	L	16694	0.07
112	2	N	16694	0.07
113	1	L	16980	0.05
113	2	O	16980	0.05
114	1	L	16650	0.07
114	2	P	16650	0.07
115	1	M	16926	0.05
115	2	N	16926	0.05
116	1	M	16802	0.06
116	2	O	16802	0.06
117	1	M	16736	0.06
117	2	P	16736	0.06
118	1	N	16664	0.07
118	2	O	16664	0.07
119	1	N	16680	0.07
119	2	P	16680	0.07
120	1	O	16754	0.06
120	2	P	16754	0.06

LS refinement shell

Resolution: 1.969→2.02 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.235	616	-
R_work	0.192	10633	-
obs	-	-	98.68 %

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