PDB-5u1a: Ferritin with Gc MtrE loop 1 inserted at His34

ID or keywords:

Entry

Database: PDB / ID: 5u1a

Title

Ferritin with Gc MtrE loop 1 inserted at His34

Components

Ferritin,MtrE protein chimera

Keywords

OXIDOREDUCTASE / chimera / nanoparticle / 24mer cage / immunogen

Function / homology

Function and homology information

bacterial non-heme ferritin / efflux transmembrane transporter activity / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / plasma membrane / cytoplasm / cytosol
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Wang, S.

Citation

Journal: FEBS Open Bio / Year: 2017
Title: Structure-based design of ferritin nanoparticle immunogens displaying antigenic loops of Neisseria gonorrhoeae.
Authors: Wang, L. / Xing, D. / Le Van, A. / Jerse, A.E. / Wang, S.

History

Deposition	Nov 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 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	5u1a.cif.gz	831.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5u1a.ent.gz	690.9 KB	Display	PDB format
PDBx/mmJSON format	5u1a.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5u1a_validation.pdf.gz	545.5 KB	Display	wwPDB validaton report
Full document	5u1a_full_validation.pdf.gz	571.1 KB	Display
Data in XML	5u1a_validation.xml.gz	87 KB	Display
Data in CIF	5u1a_validation.cif.gz	123.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/5u1a ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u1a	HTTPS FTP

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Related structure data

Related structure data	5u1bC 3bvfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4itw-1 3bvl-1 3egm-1 3bvi-1 3bvk-1 3bvf-1 3ka8-1 4zkx-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
Related items in Molecule of the Month	#222 - Jun 2018 Proteins and Nanoparticles similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (3) #35 - Nov 2002 Ferritin and Transferrin similarity (6) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (3)
#35 - Nov 2002
Ferritin and Transferrin
similarity (6)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#114 - Jun 2009
Vaults
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)

Deposited unit

A: Ferritin,MtrE protein chimera

B: Ferritin,MtrE protein chimera

C: Ferritin,MtrE protein chimera

D: Ferritin,MtrE protein chimera

E: Ferritin,MtrE protein chimera

F: Ferritin,MtrE protein chimera

G: Ferritin,MtrE protein chimera

H: Ferritin,MtrE protein chimera

I: Ferritin,MtrE protein chimera

J: Ferritin,MtrE protein chimera

K: Ferritin,MtrE protein chimera

L: Ferritin,MtrE protein chimera

hetero molecules

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

1

A: Ferritin,MtrE protein chimera

B: Ferritin,MtrE protein chimera

C: Ferritin,MtrE protein chimera

D: Ferritin,MtrE protein chimera

E: Ferritin,MtrE protein chimera

F: Ferritin,MtrE protein chimera

hetero molecules

A: Ferritin,MtrE protein chimera

B: Ferritin,MtrE protein chimera

C: Ferritin,MtrE protein chimera

D: Ferritin,MtrE protein chimera

E: Ferritin,MtrE protein chimera

F: Ferritin,MtrE protein chimera

hetero molecules

A: Ferritin,MtrE protein chimera

B: Ferritin,MtrE protein chimera

C: Ferritin,MtrE protein chimera

D: Ferritin,MtrE protein chimera

E: Ferritin,MtrE protein chimera

F: Ferritin,MtrE protein chimera

hetero molecules

A: Ferritin,MtrE protein chimera

B: Ferritin,MtrE protein chimera

C: Ferritin,MtrE protein chimera

D: Ferritin,MtrE protein chimera

E: Ferritin,MtrE protein chimera

F: Ferritin,MtrE protein chimera

hetero molecules

defined by author&software
503 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Ferritin,MtrE protein chimera

H: Ferritin,MtrE protein chimera

I: Ferritin,MtrE protein chimera

J: Ferritin,MtrE protein chimera

K: Ferritin,MtrE protein chimera

L: Ferritin,MtrE protein chimera

hetero molecules

G: Ferritin,MtrE protein chimera

H: Ferritin,MtrE protein chimera

I: Ferritin,MtrE protein chimera

J: Ferritin,MtrE protein chimera

K: Ferritin,MtrE protein chimera

L: Ferritin,MtrE protein chimera

hetero molecules

G: Ferritin,MtrE protein chimera

H: Ferritin,MtrE protein chimera

I: Ferritin,MtrE protein chimera

J: Ferritin,MtrE protein chimera

K: Ferritin,MtrE protein chimera

L: Ferritin,MtrE protein chimera

hetero molecules

G: Ferritin,MtrE protein chimera

H: Ferritin,MtrE protein chimera

I: Ferritin,MtrE protein chimera

J: Ferritin,MtrE protein chimera

K: Ferritin,MtrE protein chimera

L: Ferritin,MtrE protein chimera

hetero molecules

defined by author&software
502 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.412, 128.412, 165.041
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	75
Space group name H-M	P4

Components on special symmetry positions

ID	Model	Components
1	1	C-204- CL
2	1	D-204- CL
3	1	E-204- FE
4	1	F-206- FE
5	1	K-203- FE
6	1	L-206- FE
7	1	E-390- HOH
8	1	E-392- HOH
9	1	F-413- HOH
10	1	F-421- HOH
11	1	K-420- HOH
12	1	L-412- HOH
13	1	L-422- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	LYS	LYS	A	A	2 - 181	2 - 181
2	1	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
1	2	MET	MET	LYS	LYS	A	A	1 - 181	1 - 181
2	2	MET	MET	LYS	LYS	C	C	1 - 181	1 - 181
1	3	LEU	LEU	ARG	ARG	A	A	2 - 180	2 - 180
2	3	LEU	LEU	ARG	ARG	D	D	2 - 180	2 - 180
1	4	LEU	LEU	LYS	LYS	A	A	2 - 181	2 - 181
2	4	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
1	5	MET	MET	LYS	LYS	A	A	1 - 181	1 - 181
2	5	MET	MET	LYS	LYS	F	F	1 - 181	1 - 181
1	6	MET	MET	LYS	LYS	A	A	1 - 181	1 - 181
2	6	MET	MET	LYS	LYS	G	G	1 - 181	1 - 181
1	7	LEU	LEU	LYS	LYS	A	A	2 - 181	2 - 181
2	7	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
1	8	MET	MET	LYS	LYS	A	A	1 - 181	1 - 181
2	8	MET	MET	LYS	LYS	I	I	1 - 181	1 - 181
1	9	LEU	LEU	ARG	ARG	A	A	2 - 180	2 - 180
2	9	LEU	LEU	ARG	ARG	J	J	2 - 180	2 - 180
1	10	LEU	LEU	ARG	ARG	A	A	2 - 180	2 - 180
2	10	LEU	LEU	ARG	ARG	K	K	2 - 180	2 - 180
1	11	LEU	LEU	LYS	LYS	A	A	2 - 181	2 - 181
2	11	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	12	LEU	LEU	ARG	ARG	B	B	2 - 180	2 - 180
2	12	LEU	LEU	ARG	ARG	C	C	2 - 180	2 - 180
1	13	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	13	LEU	LEU	LYS	LYS	D	D	2 - 181	2 - 181
1	14	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	14	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
1	15	LEU	LEU	ARG	ARG	B	B	2 - 180	2 - 180
2	15	LEU	LEU	ARG	ARG	F	F	2 - 180	2 - 180
1	16	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	16	LEU	LEU	LYS	LYS	G	G	2 - 181	2 - 181
1	17	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	17	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
1	18	LEU	LEU	ARG	ARG	B	B	2 - 180	2 - 180
2	18	LEU	LEU	ARG	ARG	I	I	2 - 180	2 - 180
1	19	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	19	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	20	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	20	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	21	LEU	LEU	LYS	LYS	B	B	2 - 181	2 - 181
2	21	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	22	LEU	LEU	SER	SER	C	C	2 - 182	2 - 182
2	22	LEU	LEU	SER	SER	D	D	2 - 182	2 - 182
1	23	LEU	LEU	LYS	LYS	C	C	2 - 181	2 - 181
2	23	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
1	24	MET	MET	LYS	LYS	C	C	1 - 181	1 - 181
2	24	MET	MET	LYS	LYS	F	F	1 - 181	1 - 181
1	25	MET	MET	LYS	LYS	C	C	1 - 181	1 - 181
2	25	MET	MET	LYS	LYS	G	G	1 - 181	1 - 181
1	26	LEU	LEU	ARG	ARG	C	C	2 - 180	2 - 180
2	26	LEU	LEU	ARG	ARG	H	H	2 - 180	2 - 180
1	27	MET	MET	SER	SER	C	C	1 - 182	1 - 182
2	27	MET	MET	SER	SER	I	I	1 - 182	1 - 182
1	28	LEU	LEU	LYS	LYS	C	C	2 - 181	2 - 181
2	28	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	29	LEU	LEU	LYS	LYS	C	C	2 - 181	2 - 181
2	29	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	30	LEU	LEU	ARG	ARG	C	C	2 - 180	2 - 180
2	30	LEU	LEU	ARG	ARG	L	L	2 - 180	2 - 180
1	31	LEU	LEU	LYS	LYS	D	D	2 - 181	2 - 181
2	31	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
1	32	LEU	LEU	ARG	ARG	D	D	2 - 180	2 - 180
2	32	LEU	LEU	ARG	ARG	F	F	2 - 180	2 - 180
1	33	LEU	LEU	ARG	ARG	D	D	2 - 180	2 - 180
2	33	LEU	LEU	ARG	ARG	G	G	2 - 180	2 - 180
1	34	LEU	LEU	LYS	LYS	D	D	2 - 181	2 - 181
2	34	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
1	35	LEU	LEU	SER	SER	D	D	2 - 182	2 - 182
2	35	LEU	LEU	SER	SER	I	I	2 - 182	2 - 182
1	36	LEU	LEU	ARG	ARG	D	D	2 - 180	2 - 180
2	36	LEU	LEU	ARG	ARG	J	J	2 - 180	2 - 180
1	37	LEU	LEU	ARG	ARG	D	D	2 - 180	2 - 180
2	37	LEU	LEU	ARG	ARG	K	K	2 - 180	2 - 180
1	38	LEU	LEU	LYS	LYS	D	D	2 - 181	2 - 181
2	38	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	39	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	39	LEU	LEU	LYS	LYS	F	F	2 - 181	2 - 181
1	40	LEU	LEU	ARG	ARG	E	E	2 - 180	2 - 180
2	40	LEU	LEU	ARG	ARG	G	G	2 - 180	2 - 180
1	41	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	41	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
1	42	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	42	LEU	LEU	LYS	LYS	I	I	2 - 181	2 - 181
1	43	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	43	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	44	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	44	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	45	LEU	LEU	LYS	LYS	E	E	2 - 181	2 - 181
2	45	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	46	MET	MET	LYS	LYS	F	F	1 - 181	1 - 181
2	46	MET	MET	LYS	LYS	G	G	1 - 181	1 - 181
1	47	LEU	LEU	ARG	ARG	F	F	2 - 180	2 - 180
2	47	LEU	LEU	ARG	ARG	H	H	2 - 180	2 - 180
1	48	MET	MET	ARG	ARG	F	F	1 - 180	1 - 180
2	48	MET	MET	ARG	ARG	I	I	1 - 180	1 - 180
1	49	LEU	LEU	LYS	LYS	F	F	2 - 181	2 - 181
2	49	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	50	LEU	LEU	LYS	LYS	F	F	2 - 181	2 - 181
2	50	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	51	LEU	LEU	LYS	LYS	F	F	2 - 181	2 - 181
2	51	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	52	LEU	LEU	LYS	LYS	G	G	2 - 181	2 - 181
2	52	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
1	53	MET	MET	LYS	LYS	G	G	1 - 181	1 - 181
2	53	MET	MET	LYS	LYS	I	I	1 - 181	1 - 181
1	54	LEU	LEU	LYS	LYS	G	G	2 - 181	2 - 181
2	54	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	55	LEU	LEU	LYS	LYS	G	G	2 - 181	2 - 181
2	55	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	56	LEU	LEU	LYS	LYS	G	G	2 - 181	2 - 181
2	56	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	57	LEU	LEU	ARG	ARG	H	H	2 - 180	2 - 180
2	57	LEU	LEU	ARG	ARG	I	I	2 - 180	2 - 180
1	58	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
2	58	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
1	59	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
2	59	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	60	LEU	LEU	LYS	LYS	H	H	2 - 181	2 - 181
2	60	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	61	LEU	LEU	ARG	ARG	I	I	2 - 180	2 - 180
2	61	LEU	LEU	ARG	ARG	J	J	2 - 180	2 - 180
1	62	LEU	LEU	ARG	ARG	I	I	2 - 180	2 - 180
2	62	LEU	LEU	ARG	ARG	K	K	2 - 180	2 - 180
1	63	LEU	LEU	ARG	ARG	I	I	2 - 180	2 - 180
2	63	LEU	LEU	ARG	ARG	L	L	2 - 180	2 - 180
1	64	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
2	64	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
1	65	LEU	LEU	LYS	LYS	J	J	2 - 181	2 - 181
2	65	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181
1	66	LEU	LEU	LYS	LYS	K	K	2 - 181	2 - 181
2	66	LEU	LEU	LYS	LYS	L	L	2 - 181	2 - 181

NCS ensembles :

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Ferritin,MtrE protein chimera Mass: 20748.170 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria), (gene. exp.) Neisseria gonorrhoeae (bacteria) Gene: AM498_04815, HPY173_00920, HPY207_01135, OA23_03490, mtrE Plasmid: pET30 / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0B2EHC8, UniProt: Q51006, UniProt: P52093*PLUS, bacterial non-heme ferritin

#1: Protein

Ferritin,MtrE protein chimera

Mass: 20748.170 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Helicobacter pylori (bacteria), (gene. exp.)

Neisseria gonorrhoeae (bacteria)
Gene: AM498_04815, HPY173_00920, HPY207_01135, OA23_03490, mtrE
Plasmid: pET30 / Production host:

Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0B2EHC8, UniProt: Q51006, UniProt: P52093*PLUS, bacterial non-heme ferritin

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Non-polymers , 5 types, 1454 molecules

#2: Chemical	... ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1398 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.99 % / Description: prism
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% glycerol, 1.6 M NaCl, 8% PEG 6000, Hepes

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Data collection

Diffraction

Mean temperature: 138 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→20 Å / Num. obs: 179122 / % possible obs: 99.8 % / Redundancy: 5.6 % / R_merge(I) obs: 0.138 / R_pim(I) all: 0.064 / R_rim(I) all: 0.153 / Χ²: 1.31 / Net I/av σ(I): 14.583 / Net I/σ(I): 7.5 / Num. measured all: 1006245

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	5.4	0.895	8966	0.69	0.423	0.991	0.984	100
2.03-2.07	5.4	0.755	8943	0.732	0.357	0.836	1.019	100
2.07-2.11	5.5	0.609	8977	0.817	0.287	0.674	1.053	100
2.11-2.15	5.5	0.536	8890	0.85	0.252	0.593	1.09	100
2.15-2.2	5.5	0.47	8967	0.88	0.221	0.52	1.122	100
2.2-2.25	5.5	0.413	8964	0.902	0.194	0.457	1.162	100
2.25-2.31	5.5	0.372	8860	0.924	0.174	0.412	1.172	100
2.31-2.37	5.6	0.333	9006	0.941	0.155	0.368	1.194	100
2.37-2.44	5.6	0.304	8922	0.947	0.142	0.336	1.221	100
2.44-2.52	5.6	0.279	9016	0.956	0.129	0.308	1.268	100
2.52-2.61	5.6	0.249	8949	0.965	0.116	0.275	1.269	100
2.61-2.71	5.6	0.22	8932	0.971	0.102	0.243	1.315	100
2.71-2.84	5.7	0.165	8938	0.982	0.076	0.182	1.334	100
2.84-2.99	5.7	0.148	9036	0.986	0.068	0.163	1.403	100
2.99-3.17	5.7	0.125	8939	0.99	0.057	0.138	1.459	100
3.17-3.42	5.8	0.102	8956	0.992	0.047	0.112	1.43	99.9
3.42-3.76	5.8	0.082	8958	0.994	0.037	0.09	1.516	99.8
3.76-4.3	5.8	0.069	8991	0.996	0.031	0.076	1.596	99.6
4.3-5.39	5.8	0.065	8947	0.996	0.029	0.072	1.695	99.3
5.39-20	5.8	0.072	8965	0.995	0.033	0.079	1.772	98.5

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
HKL		data scaling
HKL		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3bvf

3bvf

Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.867 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1961	9002	5 %	RANDOM
R_work	0.1681	-	-	-
obs	0.1695	170104	99.72 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 106.89 Å² / B_iso mean: 27.607 Å² / B_iso min: 11.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.44 Å²

Refinement step

Cycle: final / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16422	0	116	1398	17936
B_iso mean	-	-	40.8	35.93	-
Num. residues	-	-	-	-	2018

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.019	16861
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15675
X-RAY DIFFRACTION	r_angle_refined_deg	2.206	1.935	22706
X-RAY DIFFRACTION	r_angle_other_deg	1.181	3	36219
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.713	5	2000
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.111	26	880
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.604	15	3067
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.396	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	2453
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	19068
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3955
X-RAY DIFFRACTION	r_mcbond_it	2.285	1.902	8054
X-RAY DIFFRACTION	r_mcbond_other	2.282	1.901	8053
X-RAY DIFFRACTION	r_mcangle_it	3.291	2.819	10027

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	11366	0.1
1	2	B	11366	0.1
2	1	A	11564	0.08
2	2	C	11564	0.08
3	1	A	11494	0.08
3	2	D	11494	0.08
4	1	A	11536	0.08
4	2	E	11536	0.08
5	1	A	11508	0.09
5	2	F	11508	0.09
6	1	A	11708	0.07
6	2	G	11708	0.07
7	1	A	11330	0.09
7	2	H	11330	0.09
8	1	A	11536	0.09
8	2	I	11536	0.09
9	1	A	11484	0.08
9	2	J	11484	0.08
10	1	A	11398	0.08
10	2	K	11398	0.08
11	1	A	11386	0.09
11	2	L	11386	0.09
12	1	B	11244	0.09
12	2	C	11244	0.09
13	1	B	11262	0.1
13	2	D	11262	0.1
14	1	B	11268	0.1
14	2	E	11268	0.1
15	1	B	11238	0.1
15	2	F	11238	0.1
16	1	B	11390	0.09
16	2	G	11390	0.09
17	1	B	11566	0.07
17	2	H	11566	0.07
18	1	B	11238	0.1
18	2	I	11238	0.1
19	1	B	11354	0.09
19	2	J	11354	0.09
20	1	B	11242	0.1
20	2	K	11242	0.1
21	1	B	11176	0.1
21	2	L	11176	0.1
22	1	C	11676	0.07
22	2	D	11676	0.07
23	1	C	11468	0.08
23	2	E	11468	0.08
24	1	C	11582	0.07
24	2	F	11582	0.07
25	1	C	11618	0.07
25	2	G	11618	0.07
26	1	C	11198	0.09
26	2	H	11198	0.09
27	1	C	11748	0.06
27	2	I	11748	0.06
28	1	C	11568	0.07
28	2	J	11568	0.07
29	1	C	11436	0.08
29	2	K	11436	0.08
30	1	C	11448	0.07
30	2	L	11448	0.07
31	1	D	11526	0.08
31	2	E	11526	0.08
32	1	D	11438	0.08
32	2	F	11438	0.08
33	1	D	11544	0.07
33	2	G	11544	0.07
34	1	D	11252	0.1
34	2	H	11252	0.1
35	1	D	11648	0.07
35	2	I	11648	0.07
36	1	D	11606	0.07
36	2	J	11606	0.07
37	1	D	11394	0.08
37	2	K	11394	0.08
38	1	D	11442	0.08
38	2	L	11442	0.08
39	1	E	11444	0.08
39	2	F	11444	0.08
40	1	E	11596	0.07
40	2	G	11596	0.07
41	1	E	11268	0.1
41	2	H	11268	0.1
42	1	E	11442	0.09
42	2	I	11442	0.09
43	1	E	11508	0.08
43	2	J	11508	0.08
44	1	E	11660	0.05
44	2	K	11660	0.05
45	1	E	11378	0.09
45	2	L	11378	0.09
46	1	F	11576	0.07
46	2	G	11576	0.07
47	1	F	11204	0.09
47	2	H	11204	0.09
48	1	F	11470	0.07
48	2	I	11470	0.07
49	1	F	11480	0.08
49	2	J	11480	0.08
50	1	F	11420	0.08
50	2	K	11420	0.08
51	1	F	11600	0.06
51	2	L	11600	0.06
52	1	G	11294	0.09
52	2	H	11294	0.09
53	1	G	11552	0.08
53	2	I	11552	0.08
54	1	G	11582	0.07
54	2	J	11582	0.07
55	1	G	11546	0.07
55	2	K	11546	0.07
56	1	G	11440	0.08
56	2	L	11440	0.08
57	1	H	11194	0.09
57	2	I	11194	0.09
58	1	H	11272	0.09
58	2	J	11272	0.09
59	1	H	11194	0.1
59	2	K	11194	0.1
60	1	H	11200	0.1
60	2	L	11200	0.1
61	1	I	11504	0.08
61	2	J	11504	0.08
62	1	I	11310	0.08
62	2	K	11310	0.08
63	1	I	11394	0.07
63	2	L	11394	0.07
64	1	J	11460	0.08
64	2	K	11460	0.08
65	1	J	11420	0.08
65	2	L	11420	0.08
66	1	K	11286	0.09
66	2	L	11286	0.09

LS refinement shell

Resolution: 2.001→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	696	-
R_work	0.25	12445	-
all	-	13141	-
obs	-	-	100 %

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	0.014	-0.0938	-0.073	0.6753	0.5115	0.6483	-0.0072	0.0061	-0.0115	0.0152	-0.0541	0.063	0.0018	-0.0357	0.0613	0.0316	-0.004	0.0086	0.0178	-0.0118	0.0491	27.965	211.4434	-24.7445
2	0.9065	-0.1304	0.7067	0.1	-0.2554	0.8613	-0.0874	0.0526	0.0901	-0.006	-0.032	-0.0279	-0.0353	0.0709	0.1194	0.0183	-0.0085	-0.0207	0.036	0.0166	0.0624	39.6833	225.5413	30.0375
3	0.0918	-0.2415	0.0113	0.823	-0.2854	0.3694	0.0155	0.0102	0.0112	-0.0497	0.0038	-0.0271	0.0269	-0.0545	-0.0193	0.0529	-0.0149	0.0083	0.0182	0.0069	0.0274	17.1442	180.2174	-6.5895
4	0.0206	0.0511	0.0597	1.5209	-0.2817	0.3893	-0.0048	0.0083	-0.0024	0.1929	0.0318	-0.0253	-0.0177	-0.0288	-0.027	0.0663	-0.0118	-0.0086	0.0331	0.0075	0.0155	15.6558	197.7345	11.6183
5	1.1295	-0.3635	0.7966	0.329	-0.2378	0.5677	0.0707	-0.0781	-0.0583	-0.0658	-0.0092	-0.0091	0.0563	-0.0555	-0.0615	0.037	-0.0081	-0.0271	0.022	0.0081	0.0523	37.5398	203.4216	42.7227
6	0.1899	-0.1367	-0.0008	0.5423	0.3358	0.2554	-0.0215	-0.0274	-0.0108	-0.0313	0.0336	-0.0112	-0.0275	0.0125	-0.0121	0.0331	0.004	0.0066	0.017	-0.0048	0.055	49.3065	217.4073	-37.042
7	0.0166	-0.0898	-0.0586	0.5491	0.3753	0.448	-0.0126	0.0046	-0.0174	0.0133	-0.0297	0.0708	-0.0031	0.0001	0.0423	0.0453	-0.0088	0.0144	0.0116	-0.0056	0.0547	90.9473	273.4038	57.8876
8	0.64	-0.0857	0.5817	0.0802	-0.2114	0.8115	-0.0621	0.0402	0.0739	-0.0101	-0.0291	-0.0142	-0.0144	0.0589	0.0913	0.0171	-0.011	-0.017	0.0376	0.0146	0.0598	101.8429	288.1258	112.602
9	0.1387	-0.2569	-0.0272	0.6972	-0.1867	0.2684	0.0157	0.0089	0.013	-0.0354	0.0008	-0.0142	0.0208	-0.0254	-0.0166	0.0473	0.0036	0.0035	0.0156	0.0055	0.0419	82.2182	241.4233	76.0896
10	0.0118	-0.0159	0.0577	1.5315	-0.0789	0.3472	-0.0061	0.0012	0.0058	0.2136	0.0212	-0.018	0.0039	-0.0271	-0.0151	0.0708	0.0024	-0.0032	0.0185	0.0186	0.0323	79.4909	258.7715	94.3572
11	1.0991	-0.3481	0.7973	0.3356	-0.2851	0.5887	0.067	-0.0639	-0.0651	-0.0544	-0.0014	0.0057	0.0592	-0.041	-0.0655	0.0241	-0.0082	-0.0227	0.0148	0.0045	0.0654	100.9873	265.9453	125.1706
12	0.1269	-0.1228	-0.0285	0.3753	0.28	0.27	-0.0106	-0.015	-0.0138	-0.032	0.0202	-0.0206	-0.0333	0.0181	-0.0096	0.0315	-0.0034	0.0098	0.021	-0.0013	0.0602	112.0654	280.4888	45.5516

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 181
2	X-RAY DIFFRACTION	2	B	2 - 181
3	X-RAY DIFFRACTION	3	C	1 - 182
4	X-RAY DIFFRACTION	4	D	2 - 182
5	X-RAY DIFFRACTION	5	E	2 - 181
6	X-RAY DIFFRACTION	6	F	1 - 181
7	X-RAY DIFFRACTION	7	G	1 - 181
8	X-RAY DIFFRACTION	8	H	2 - 181
9	X-RAY DIFFRACTION	9	I	1 - 182
10	X-RAY DIFFRACTION	10	J	2 - 181
11	X-RAY DIFFRACTION	11	K	2 - 181
12	X-RAY DIFFRACTION	12	L	2 - 181

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