PDB-12jr: Designed pentameric proton channel LQLL I6S/I13S

ID or keywords:

Entry

Database: PDB / ID: 12jr

Title

Designed pentameric proton channel LQLL I6S/I13S

Components

Proton channel LQLL I6S/I13S

Keywords

MEMBRANE PROTEIN / proton channel / helical bundle / designed protein

Function / homology

TRIETHYLENE GLYCOL

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Jacob, N.P. / Kratochvil, H.T.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction
Authors: Jacob, N.P. / Silverman, V.T. / Prida, G. / Kratochvil, H.T.

History

Deposition	Apr 8, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2026	Provider: repository / Type: Initial release
Revision 2.0	Aug 26, 2026	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary Category: atom_site / atom_type ...atom_site / atom_type / pdbx_contact_author / pdbx_struct_assembly_prop / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software Item: _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi ..._pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_restr_ncs.weight_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.version Description: Atoms with unrealistic or zero occupancies / Details: Hydrogens have been removed / Provider: author / Type: Coordinate replacement

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	12jr.cif.gz	66 KB	Display	PDBx/mmCIF format
PDB format	pdb12jr.ent.gz	47.2 KB	Display	PDB format
PDBx/mmJSON format	12jr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2j/12jr ftp://data.pdbj.org/pub/pdb/validation_reports/2j/12jr	HTTPS FTP

-
Related structure data

Related structure data	12jsC 12kiC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Proton channel LQLL I6S/I13S

B: Proton channel LQLL I6S/I13S

C: Proton channel LQLL I6S/I13S

D: Proton channel LQLL I6S/I13S

E: Proton channel LQLL I6S/I13S

F: Proton channel LQLL I6S/I13S

G: Proton channel LQLL I6S/I13S

H: Proton channel LQLL I6S/I13S

I: Proton channel LQLL I6S/I13S

J: Proton channel LQLL I6S/I13S

hetero molecules

30.3 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Proton channel LQLL I6S/I13S

B: Proton channel LQLL I6S/I13S

C: Proton channel LQLL I6S/I13S

D: Proton channel LQLL I6S/I13S

E: Proton channel LQLL I6S/I13S

hetero molecules

defined by author&software
Evidence: Assembly was confirmed using denaturing SDS gel electrophoresis
15.1 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Proton channel LQLL I6S/I13S

G: Proton channel LQLL I6S/I13S

H: Proton channel LQLL I6S/I13S

I: Proton channel LQLL I6S/I13S

J: Proton channel LQLL I6S/I13S

hetero molecules

defined by author&software
15.2 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.864, 45.093, 47.515
Angle α, β, γ (deg.)	117.733, 99.481, 106.016
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
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	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	GLY	GLY	A	A	2 - 26	2 - 26
2	1	1	SER	SER	GLY	GLY	B	B	2 - 26	2 - 26
3	2	2	SER	SER	LEU	LEU	A	A	2 - 24	2 - 24
4	2	2	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
5	3	3	SER	SER	GLY	GLY	A	A	2 - 26	2 - 26
6	3	3	SER	SER	GLY	GLY	D	D	2 - 26	2 - 26
7	4	4	SER	SER	ARG	ARG	A	A	2 - 25	2 - 25
8	4	4	SER	SER	ARG	ARG	E	E	2 - 25	2 - 25
9	5	5	SER	SER	LEU	LEU	A	A	2 - 24	2 - 24
10	5	5	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
11	6	6	SER	SER	ARG	ARG	A	A	2 - 25	2 - 25
12	6	6	SER	SER	ARG	ARG	G	G	2 - 25	2 - 25
13	7	7	SER	SER	GLY	GLY	A	A	2 - 26	2 - 26
14	7	7	SER	SER	GLY	GLY	H	H	2 - 26	2 - 26
15	8	8	SER	SER	LEU	LEU	A	A	2 - 24	2 - 24
16	8	8	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
17	9	9	SER	SER	LEU	LEU	A	A	2 - 24	2 - 24
18	9	9	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
19	10	10	SER	SER	LEU	LEU	B	B	2 - 24	2 - 24
20	10	10	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
21	11	11	SER	SER	GLY	GLY	B	B	2 - 26	2 - 26
22	11	11	SER	SER	GLY	GLY	D	D	2 - 26	2 - 26
23	12	12	SER	SER	ARG	ARG	B	B	2 - 25	2 - 25
24	12	12	SER	SER	ARG	ARG	E	E	2 - 25	2 - 25
25	13	13	SER	SER	LEU	LEU	B	B	2 - 24	2 - 24
26	13	13	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
27	14	14	SER	SER	ARG	ARG	B	B	2 - 25	2 - 25
28	14	14	SER	SER	ARG	ARG	G	G	2 - 25	2 - 25
29	15	15	SER	SER	GLY	GLY	B	B	2 - 26	2 - 26
30	15	15	SER	SER	GLY	GLY	H	H	2 - 26	2 - 26
31	16	16	SER	SER	LEU	LEU	B	B	2 - 24	2 - 24
32	16	16	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
33	17	17	SER	SER	LEU	LEU	B	B	2 - 24	2 - 24
34	17	17	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
35	18	18	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
36	18	18	SER	SER	LEU	LEU	D	D	2 - 24	2 - 24
37	19	19	ASP	ASP	LEU	LEU	C	C	1 - 24	1 - 24
38	19	19	ASP	ASP	LEU	LEU	E	E	1 - 24	1 - 24
39	20	20	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
40	20	20	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
41	21	21	ASP	ASP	LEU	LEU	C	C	1 - 24	1 - 24
42	21	21	ASP	ASP	LEU	LEU	G	G	1 - 24	1 - 24
43	22	22	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
44	22	22	SER	SER	LEU	LEU	H	H	2 - 24	2 - 24
45	23	23	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
46	23	23	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
47	24	24	SER	SER	LEU	LEU	C	C	2 - 24	2 - 24
48	24	24	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
49	25	25	SER	SER	ARG	ARG	D	D	2 - 25	2 - 25
50	25	25	SER	SER	ARG	ARG	E	E	2 - 25	2 - 25
51	26	26	SER	SER	LEU	LEU	D	D	2 - 24	2 - 24
52	26	26	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
53	27	27	SER	SER	ARG	ARG	D	D	2 - 25	2 - 25
54	27	27	SER	SER	ARG	ARG	G	G	2 - 25	2 - 25
55	28	28	SER	SER	GLY	GLY	D	D	2 - 26	2 - 26
56	28	28	SER	SER	GLY	GLY	H	H	2 - 26	2 - 26
57	29	29	SER	SER	LEU	LEU	D	D	2 - 24	2 - 24
58	29	29	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
59	30	30	SER	SER	LEU	LEU	D	D	2 - 24	2 - 24
60	30	30	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
61	31	31	SER	SER	LEU	LEU	E	E	2 - 24	2 - 24
62	31	31	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
63	32	32	ASP	ASP	GLY	GLY	E	E	1 - 26	1 - 26
64	32	32	ASP	ASP	GLY	GLY	G	G	1 - 26	1 - 26
65	33	33	SER	SER	ARG	ARG	E	E	2 - 25	2 - 25
66	33	33	SER	SER	ARG	ARG	H	H	2 - 25	2 - 25
67	34	34	SER	SER	LEU	LEU	E	E	2 - 24	2 - 24
68	34	34	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
69	35	35	SER	SER	LEU	LEU	E	E	2 - 24	2 - 24
70	35	35	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
71	36	36	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
72	36	36	SER	SER	LEU	LEU	G	G	2 - 24	2 - 24
73	37	37	SER	SER	LEU	LEU	F	F	2 - 24	2 - 24
74	37	37	SER	SER	LEU	LEU	H	H	2 - 24	2 - 24
75	38	38	SER	SER	ARG	ARG	F	F	2 - 25	2 - 25
76	38	38	SER	SER	ARG	ARG	I	I	2 - 25	2 - 25
77	39	39	SER	SER	ARG	ARG	F	F	2 - 25	2 - 25
78	39	39	SER	SER	ARG	ARG	J	J	2 - 25	2 - 25
79	40	40	SER	SER	ARG	ARG	G	G	2 - 25	2 - 25
80	40	40	SER	SER	ARG	ARG	H	H	2 - 25	2 - 25
81	41	41	SER	SER	LEU	LEU	G	G	2 - 24	2 - 24
82	41	41	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
83	42	42	SER	SER	LEU	LEU	G	G	2 - 24	2 - 24
84	42	42	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
85	43	43	SER	SER	LEU	LEU	H	H	2 - 24	2 - 24
86	43	43	SER	SER	LEU	LEU	I	I	2 - 24	2 - 24
87	44	44	SER	SER	LEU	LEU	H	H	2 - 24	2 - 24
88	44	44	SER	SER	LEU	LEU	J	J	2 - 24	2 - 24
89	45	45	SER	SER	ARG	ARG	I	I	2 - 25	2 - 25
90	45	45	SER	SER	ARG	ARG	J	J	2 - 25	2 - 25

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72
37	Local NCS retraints between domains: 73 74
38	Local NCS retraints between domains: 75 76
39	Local NCS retraints between domains: 77 78
40	Local NCS retraints between domains: 79 80
41	Local NCS retraints between domains: 81 82
42	Local NCS retraints between domains: 83 84
43	Local NCS retraints between domains: 85 86
44	Local NCS retraints between domains: 87 88
45	Local NCS retraints between domains: 89 90

#1: Protein/peptide	Proton channel LQLL I6S/I13S Mass: 2993.670 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.73 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase Details: 0.1M NaCl, 0.1M HEPES pH 7.5, 12% PEG 4K, 30% PEG 400 Cryoprotectant

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.87→39.403 Å / Num. obs: 18360 / % possible obs: 81.9 % / Redundancy: 3.9 % / CC_1/2: 0.998 / Net I/σ(I): 5.61
Reflection shell	Resolution: 1.87→1.91 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 955 / CC_1/2: 0.117 / % possible all: 64.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.128)	refinement
Aimless	0.8.2	data scaling
DIALS	3.dev.1265-g3515746c1	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→39.403 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.913 / WR_factor R_free: 0.241 / WR_factor R_work: 0.221 / SU B: 6.541 / SU ML: 0.164 / Average fsc free: 0.9641 / Average fsc work: 0.9743 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.262 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2433	566	5.141 %	RANDOM
R_work	0.2134	10443	-	-
all	0.215	-	-	-
obs	-	11009	85.653 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.397 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.427 Å²	-0.731 Å²	0.11 Å²
2-	-	0.197 Å²	-0.652 Å²
3-	-	-	0.356 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→39.403 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2034	0	23	1	2058

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2134
X-RAY DIFFRACTION	r_angle_refined_deg	1.265	1.787	2891
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.438	5	245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.557	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.697	10	381
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.215	10	63
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	376
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1487
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1052
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	1510
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.06	0.2	67
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.386	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.558	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.792	3.251	1001
X-RAY DIFFRACTION	r_mcangle_it	7.568	5.735	1239
X-RAY DIFFRACTION	r_scbond_it	8.207	4.225	1133
X-RAY DIFFRACTION	r_scangle_it	11.243	7.387	1652
X-RAY DIFFRACTION	r_lrange_it	13.43	54.566	3437
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.079	0.05	744
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	712
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.116	0.05	749
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.081	0.05	745
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	707
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.065	0.05	753
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.108	0.05	736
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.076	0.05	712
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.055	0.05	719
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.075	0.05	708
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.092	0.05	737
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.058	0.05	734
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.063	0.05	710
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.087	0.05	730
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.093	0.05	741
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.065	0.05	710
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.07	0.05	707
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.079	0.05	730
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.068	0.05	759
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.071	0.05	729
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.026	0.05	788
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.073	0.05	741
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.04	0.05	748
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.077	0.05	737
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.104	0.05	731
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.09	0.05	704
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.108	0.05	737
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.077	0.05	736
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.083	0.05	701
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.085	0.05	707
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.055	0.05	715
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.103	0.05	785
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.085	0.05	728
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.08	0.05	712
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.071	0.05	714
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.07	0.05	734
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.053	0.05	733
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.085	0.05	774
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.082	0.05	770
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.082	0.05	728
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.059	0.05	720
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.081	0.05	716
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.082	0.05	709
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.096	0.05	708
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.081	0.05	796

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07919	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07919	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0638	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.0638	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11638	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.11638	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08095	0.05007
4	8	E	X-RAY DIFFRACTION	Local ncs	0.08095	0.05007
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09179	0.05008
5	10	F	X-RAY DIFFRACTION	Local ncs	0.09179	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06532	0.05008
6	12	G	X-RAY DIFFRACTION	Local ncs	0.06532	0.05008
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10778	0.05008
7	14	H	X-RAY DIFFRACTION	Local ncs	0.10778	0.05008
8	15	A	X-RAY DIFFRACTION	Local ncs	0.07552	0.05008
8	16	I	X-RAY DIFFRACTION	Local ncs	0.07552	0.05008
9	17	A	X-RAY DIFFRACTION	Local ncs	0.05458	0.05008
9	18	J	X-RAY DIFFRACTION	Local ncs	0.05458	0.05008
10	19	B	X-RAY DIFFRACTION	Local ncs	0.07474	0.05007
10	20	C	X-RAY DIFFRACTION	Local ncs	0.07474	0.05007
11	21	B	X-RAY DIFFRACTION	Local ncs	0.09234	0.05007
11	22	D	X-RAY DIFFRACTION	Local ncs	0.09234	0.05007
12	23	B	X-RAY DIFFRACTION	Local ncs	0.05838	0.05007
12	24	E	X-RAY DIFFRACTION	Local ncs	0.05838	0.05007
13	25	B	X-RAY DIFFRACTION	Local ncs	0.06341	0.05008
13	26	F	X-RAY DIFFRACTION	Local ncs	0.06341	0.05008
14	27	B	X-RAY DIFFRACTION	Local ncs	0.08703	0.05007
14	28	G	X-RAY DIFFRACTION	Local ncs	0.08703	0.05007
15	29	B	X-RAY DIFFRACTION	Local ncs	0.09333	0.05007
15	30	H	X-RAY DIFFRACTION	Local ncs	0.09333	0.05007
16	31	B	X-RAY DIFFRACTION	Local ncs	0.06497	0.05007
16	32	I	X-RAY DIFFRACTION	Local ncs	0.06497	0.05007
17	33	B	X-RAY DIFFRACTION	Local ncs	0.07031	0.05007
17	34	J	X-RAY DIFFRACTION	Local ncs	0.07031	0.05007
18	35	C	X-RAY DIFFRACTION	Local ncs	0.07949	0.05008
18	36	D	X-RAY DIFFRACTION	Local ncs	0.07949	0.05008
19	37	C	X-RAY DIFFRACTION	Local ncs	0.06762	0.05008
19	38	E	X-RAY DIFFRACTION	Local ncs	0.06762	0.05008
20	39	C	X-RAY DIFFRACTION	Local ncs	0.07052	0.05008
20	40	F	X-RAY DIFFRACTION	Local ncs	0.07052	0.05008
21	41	C	X-RAY DIFFRACTION	Local ncs	0.02621	0.05008
21	42	G	X-RAY DIFFRACTION	Local ncs	0.02621	0.05008
22	43	C	X-RAY DIFFRACTION	Local ncs	0.07319	0.05008
22	44	H	X-RAY DIFFRACTION	Local ncs	0.07319	0.05008
23	45	C	X-RAY DIFFRACTION	Local ncs	0.0398	0.05008
23	46	I	X-RAY DIFFRACTION	Local ncs	0.0398	0.05008
24	47	C	X-RAY DIFFRACTION	Local ncs	0.07705	0.05008
24	48	J	X-RAY DIFFRACTION	Local ncs	0.07705	0.05008
25	49	D	X-RAY DIFFRACTION	Local ncs	0.10359	0.05008
25	50	E	X-RAY DIFFRACTION	Local ncs	0.10359	0.05008
26	51	D	X-RAY DIFFRACTION	Local ncs	0.09033	0.05008
26	52	F	X-RAY DIFFRACTION	Local ncs	0.09033	0.05008
27	53	D	X-RAY DIFFRACTION	Local ncs	0.1082	0.05008
27	54	G	X-RAY DIFFRACTION	Local ncs	0.1082	0.05008
28	55	D	X-RAY DIFFRACTION	Local ncs	0.07653	0.05008
28	56	H	X-RAY DIFFRACTION	Local ncs	0.07653	0.05008
29	57	D	X-RAY DIFFRACTION	Local ncs	0.08304	0.05008
29	58	I	X-RAY DIFFRACTION	Local ncs	0.08304	0.05008
30	59	D	X-RAY DIFFRACTION	Local ncs	0.08502	0.05008
30	60	J	X-RAY DIFFRACTION	Local ncs	0.08502	0.05008
31	61	E	X-RAY DIFFRACTION	Local ncs	0.05528	0.05008
31	62	F	X-RAY DIFFRACTION	Local ncs	0.05528	0.05008
32	63	E	X-RAY DIFFRACTION	Local ncs	0.1032	0.05007
32	64	G	X-RAY DIFFRACTION	Local ncs	0.1032	0.05007
33	65	E	X-RAY DIFFRACTION	Local ncs	0.08476	0.05008
33	66	H	X-RAY DIFFRACTION	Local ncs	0.08476	0.05008
34	67	E	X-RAY DIFFRACTION	Local ncs	0.08021	0.05008
34	68	I	X-RAY DIFFRACTION	Local ncs	0.08021	0.05008
35	69	E	X-RAY DIFFRACTION	Local ncs	0.07085	0.05008
35	70	J	X-RAY DIFFRACTION	Local ncs	0.07085	0.05008
36	71	F	X-RAY DIFFRACTION	Local ncs	0.0695	0.05008
36	72	G	X-RAY DIFFRACTION	Local ncs	0.0695	0.05008
37	73	F	X-RAY DIFFRACTION	Local ncs	0.05308	0.05008
37	74	H	X-RAY DIFFRACTION	Local ncs	0.05308	0.05008
38	75	F	X-RAY DIFFRACTION	Local ncs	0.08497	0.05007
38	76	I	X-RAY DIFFRACTION	Local ncs	0.08497	0.05007
39	77	F	X-RAY DIFFRACTION	Local ncs	0.08189	0.05008
39	78	J	X-RAY DIFFRACTION	Local ncs	0.08189	0.05008
40	79	G	X-RAY DIFFRACTION	Local ncs	0.08247	0.05008
40	80	H	X-RAY DIFFRACTION	Local ncs	0.08247	0.05008
41	81	G	X-RAY DIFFRACTION	Local ncs	0.05891	0.05008
41	82	I	X-RAY DIFFRACTION	Local ncs	0.05891	0.05008
42	83	G	X-RAY DIFFRACTION	Local ncs	0.08064	0.05008
42	84	J	X-RAY DIFFRACTION	Local ncs	0.08064	0.05008
43	85	H	X-RAY DIFFRACTION	Local ncs	0.08244	0.05008
43	86	I	X-RAY DIFFRACTION	Local ncs	0.08244	0.05008
44	87	H	X-RAY DIFFRACTION	Local ncs	0.09577	0.05008
44	88	J	X-RAY DIFFRACTION	Local ncs	0.09577	0.05008
45	89	I	X-RAY DIFFRACTION	Local ncs	0.08076	0.05008
45	90	J	X-RAY DIFFRACTION	Local ncs	0.08076	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.25-2.308	0.264	50	0.244	825	0.245	932	0.945	0.956	93.8841	0.22
2.308-2.371	0.225	51	0.203	833	0.204	951	0.966	0.973	92.9548	0.176
2.371-2.44	0.297	52	0.201	756	0.206	868	0.949	0.974	93.0876	0.181
2.44-2.515	0.167	31	0.194	791	0.193	902	0.987	0.975	91.1308	0.166
2.515-2.597	0.235	36	0.183	711	0.186	823	0.965	0.976	90.7655	0.164
2.597-2.687	0.169	21	0.185	526	0.184	825	0.984	0.978	66.303	0.161
2.687-2.788	0.198	30	0.175	680	0.176	788	0.977	0.98	90.1015	0.155
2.788-2.902	0.238	38	0.181	615	0.184	766	0.969	0.98	85.248	0.156
2.902-3.03	0.222	43	0.172	537	0.176	737	0.967	0.982	78.6974	0.156
3.03-3.177	0.211	30	0.191	575	0.192	698	0.977	0.981	86.6762	0.17
3.177-3.347	0.182	27	0.181	594	0.181	650	0.979	0.982	95.5385	0.164
3.347-3.549	0.388	27	0.22	406	0.229	625	0.922	0.973	69.28	0.204
3.549-3.792	0.198	22	0.227	376	0.225	595	0.982	0.97	66.8908	0.23
3.792-4.092	0.232	20	0.201	360	0.202	551	0.959	0.977	68.9655	0.211
4.092-4.478	0.232	23	0.235	442	0.235	501	0.969	0.975	92.8144	0.245
4.478-4.999	0.279	17	0.24	408	0.241	461	0.962	0.973	92.1909	0.255
4.999-5.757	0.442	16	0.26	326	0.266	419	0.923	0.964	81.6229	0.29
5.757-7.013	0.284	13	0.292	283	0.291	332	0.974	0.962	89.1566	0.313
7.013-9.764	0.189	16	0.183	254	0.183	274	0.989	0.989	98.5401	0.257
9.764-39.403	0.291	3	0.278	143	0.278	152	0.938	0.952	96.0526	0.481

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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