PDB-8ail: Bacillus phage VMY22 p56 in complex with Bacillus weidmannii Ung

ID or keywords:

Entry

Database: PDB / ID: 8ail

Title

Bacillus phage VMY22 p56 in complex with Bacillus weidmannii Ung

Components

Bacillus phage VMY22 p56
Uracil-DNA glycosylase

Keywords

PROTEIN BINDING / Inhibitor / Complex / UDG / Ung

Function / homology

Function and homology information

uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm
Similarity search - Function

Biological species

Bacillus wiedmannii (bacteria)

Bacillus phage VMY22 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Muselmani, W. / Bagneris, C. / Savva, R.

Funding support

United Kingdom, 1items

Citation

Journal: Viruses / Year: 2023
Title: A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase.
Authors: Muselmani, W. / Kashif-Khan, N. / Bagneris, C. / Santangelo, R. / Williams, M.A. / Savva, R.

History

Deposition	Jul 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ail.cif.gz	529.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8ail.ent.gz	428 KB	Display	PDB format
PDBx/mmJSON format	8ail.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ail_validation.pdf.gz	499.5 KB	Display	wwPDB validaton report
Full document	8ail_full_validation.pdf.gz	507.3 KB	Display
Data in XML	8ail_validation.xml.gz	44.7 KB	Display
Data in CIF	8ail_validation.cif.gz	62.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/8ail ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8ail	HTTPS FTP

-
Related structure data

Related structure data	8aimC 8ainC 4l5nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

I: Uracil-DNA glycosylase

M: Uracil-DNA glycosylase

A: Uracil-DNA glycosylase

B: Uracil-DNA glycosylase

O: Bacillus phage VMY22 p56

E: Bacillus phage VMY22 p56

F: Bacillus phage VMY22 p56

J: Bacillus phage VMY22 p56

N: Bacillus phage VMY22 p56

C: Bacillus phage VMY22 p56

K: Bacillus phage VMY22 p56

D: Bacillus phage VMY22 p56

hetero molecules

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

1

I: Uracil-DNA glycosylase

M: Uracil-DNA glycosylase

O: Bacillus phage VMY22 p56

J: Bacillus phage VMY22 p56

N: Bacillus phage VMY22 p56

K: Bacillus phage VMY22 p56

hetero molecules

defined by author&software
79.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Uracil-DNA glycosylase

B: Uracil-DNA glycosylase

E: Bacillus phage VMY22 p56

F: Bacillus phage VMY22 p56

C: Bacillus phage VMY22 p56

D: Bacillus phage VMY22 p56

hetero molecules

defined by author&software
79.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.327, 97.495, 100.555
Angle α, β, γ (deg.)	90.000, 111.362, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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	ASN	ASN	ASN	ASN	I	A	3 - 224	3 - 224
2	2	1	ASN	ASN	ASN	ASN	M	B	3 - 224	3 - 224
3	3	2	MET	MET	LEU	LEU	I	A	1 - 225	1 - 225
4	4	2	MET	MET	LEU	LEU	A	C	1 - 225	1 - 225
5	5	3	MET	MET	LEU	LEU	I	A	1 - 225	1 - 225
6	6	3	MET	MET	LEU	LEU	B	D	1 - 225	1 - 225
7	7	4	ASN	ASN	ASN	ASN	M	B	3 - 224	3 - 224
8	8	4	ASN	ASN	ASN	ASN	A	C	3 - 224	3 - 224
9	9	5	ASN	ASN	ASN	ASN	M	B	3 - 224	3 - 224
10	10	5	ASN	ASN	ASN	ASN	B	D	3 - 224	3 - 224
11	11	6	MET	MET	LEU	LEU	A	C	1 - 225	1 - 225
12	12	6	MET	MET	LEU	LEU	B	D	1 - 225	1 - 225
13	13	7	MET	MET	PHE	PHE	O	E	1 - 56	1 - 56
14	14	7	MET	MET	PHE	PHE	E	F	1 - 56	1 - 56
15	15	8	PHE	PHE	MET	MET	O	E	4 - 55	4 - 55
16	16	8	PHE	PHE	MET	MET	F	G	4 - 55	4 - 55
17	17	9	PHE	PHE	MET	MET	O	E	4 - 55	4 - 55
18	18	9	PHE	PHE	MET	MET	J	H	4 - 55	4 - 55
19	19	10	PHE	PHE	MET	MET	O	E	4 - 55	4 - 55
20	20	10	PHE	PHE	MET	MET	N	I	4 - 55	4 - 55
21	21	11	ASP	ASP	MET	MET	O	E	6 - 55	6 - 55
22	22	11	ASP	ASP	MET	MET	C	J	6 - 55	6 - 55
23	23	12	ASP	ASP	MET	MET	O	E	6 - 55	6 - 55
24	24	12	ASP	ASP	MET	MET	K	K	6 - 55	6 - 55
25	25	13	ASP	ASP	MET	MET	O	E	6 - 55	6 - 55
26	26	13	ASP	ASP	MET	MET	D	L	6 - 55	6 - 55
27	27	14	PHE	PHE	MET	MET	E	F	4 - 55	4 - 55
28	28	14	PHE	PHE	MET	MET	F	G	4 - 55	4 - 55
29	29	15	PHE	PHE	MET	MET	E	F	4 - 55	4 - 55
30	30	15	PHE	PHE	MET	MET	J	H	4 - 55	4 - 55
31	31	16	PHE	PHE	MET	MET	E	F	4 - 55	4 - 55
32	32	16	PHE	PHE	MET	MET	N	I	4 - 55	4 - 55
33	33	17	ASP	ASP	MET	MET	E	F	6 - 55	6 - 55
34	34	17	ASP	ASP	MET	MET	C	J	6 - 55	6 - 55
35	35	18	ASP	ASP	MET	MET	E	F	6 - 55	6 - 55
36	36	18	ASP	ASP	MET	MET	K	K	6 - 55	6 - 55
37	37	19	ASP	ASP	MET	MET	E	F	6 - 55	6 - 55
38	38	19	ASP	ASP	MET	MET	D	L	6 - 55	6 - 55
39	39	20	PHE	PHE	PHE	PHE	F	G	4 - 56	4 - 56
40	40	20	PHE	PHE	PHE	PHE	J	H	4 - 56	4 - 56
41	41	21	PHE	PHE	PHE	PHE	F	G	4 - 56	4 - 56
42	42	21	PHE	PHE	PHE	PHE	N	I	4 - 56	4 - 56
43	43	22	ASP	ASP	MET	MET	F	G	6 - 55	6 - 55
44	44	22	ASP	ASP	MET	MET	C	J	6 - 55	6 - 55
45	45	23	ASP	ASP	MET	MET	F	G	6 - 55	6 - 55
46	46	23	ASP	ASP	MET	MET	K	K	6 - 55	6 - 55
47	47	24	ASP	ASP	MET	MET	F	G	6 - 55	6 - 55
48	48	24	ASP	ASP	MET	MET	D	L	6 - 55	6 - 55
49	49	25	PHE	PHE	PHE	PHE	J	H	4 - 56	4 - 56
50	50	25	PHE	PHE	PHE	PHE	N	I	4 - 56	4 - 56
51	51	26	ASP	ASP	MET	MET	J	H	6 - 55	6 - 55
52	52	26	ASP	ASP	MET	MET	C	J	6 - 55	6 - 55
53	53	27	ASP	ASP	MET	MET	J	H	6 - 55	6 - 55
54	54	27	ASP	ASP	MET	MET	K	K	6 - 55	6 - 55
55	55	28	ASP	ASP	MET	MET	J	H	6 - 55	6 - 55
56	56	28	ASP	ASP	MET	MET	D	L	6 - 55	6 - 55
57	57	29	ASP	ASP	MET	MET	N	I	6 - 55	6 - 55
58	58	29	ASP	ASP	MET	MET	C	J	6 - 55	6 - 55
59	59	30	ASP	ASP	MET	MET	N	I	6 - 55	6 - 55
60	60	30	ASP	ASP	MET	MET	K	K	6 - 55	6 - 55
61	61	31	ASP	ASP	MET	MET	N	I	6 - 55	6 - 55
62	62	31	ASP	ASP	MET	MET	D	L	6 - 55	6 - 55
63	63	32	ASP	ASP	PHE	PHE	C	J	6 - 56	6 - 56
64	64	32	ASP	ASP	PHE	PHE	K	K	6 - 56	6 - 56
65	65	33	ASP	ASP	PHE	PHE	C	J	6 - 56	6 - 56
66	66	33	ASP	ASP	PHE	PHE	D	L	6 - 56	6 - 56
67	67	34	ASP	ASP	PHE	PHE	K	K	6 - 56	6 - 56
68	68	34	ASP	ASP	PHE	PHE	D	L	6 - 56	6 - 56

NCS ensembles :

ID	Details
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

#1: Protein	Uracil-DNA glycosylase / UDG Mass: 26043.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus wiedmannii (bacteria) / Gene: ung, COF57_03435 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2C5A1M3, uracil-DNA glycosylase
#2: Protein	Bacillus phage VMY22 p56 Mass: 6723.735 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage VMY22 (virus) / Gene: VMY22_4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9SK00
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.12 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium iodide, 0.1M Bis-tris propane pH 6.5, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 289.15 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.45→48.87 Å / Num. obs: 56337 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC_1/2: 0.993 / Net I/σ(I): 2.53
Reflection shell	Resolution: 2.45→2.52 Å / Num. unique obs: 4587 / CC_1/2: 0.821

-
Processing

Software

Name	Version	Classification
REFMAC	5.8	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L5N

4l5n

Resolution: 2.45→48.87 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.919 / SU B: 9.41 / SU ML: 0.203 / Cross valid method: FREE R-VALUE / ESU R: 0.56 / ESU R Free: 0.269

	R_factor	Num. reflection	% reflection
R_free	0.237	2745	4.874 %
R_work	0.2044	53573	-
all	0.206	-	-
obs	-	56318	99.674 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.146 Å²	0 Å²	-0.308 Å²
2-	-	1.136 Å²	-0 Å²
3-	-	-	-0.797 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→48.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10913	0	52	129	11094

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	11214
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10531
X-RAY DIFFRACTION	r_angle_refined_deg	1.413	1.646	15159
X-RAY DIFFRACTION	r_angle_other_deg	1.189	1.58	24353
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.505	5	1310
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.749	23.937	602
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.121	15	2034
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.77	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1424
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	12517
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2499
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	1913
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	9517
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	5188
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	5163
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	264
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.073	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.121	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.24	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.396	3.462	5276
X-RAY DIFFRACTION	r_mcbond_other	2.396	3.462	5275
X-RAY DIFFRACTION	r_mcangle_it	3.676	5.185	6574
X-RAY DIFFRACTION	r_mcangle_other	3.676	5.185	6575
X-RAY DIFFRACTION	r_scbond_it	2.828	3.793	5938
X-RAY DIFFRACTION	r_scbond_other	2.826	3.793	5938
X-RAY DIFFRACTION	r_scangle_it	4.458	5.549	8585
X-RAY DIFFRACTION	r_scangle_other	4.457	5.548	8585
X-RAY DIFFRACTION	r_lrange_it	5.985	38.62	12009
X-RAY DIFFRACTION	r_lrange_other	5.984	38.626	11995
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	7368
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.073	0.05	7439
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.058	0.05	7491
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.071	0.05	7355
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.075	0.05	7348
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.08	0.05	7449
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.084	0.05	1626
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.118	0.05	1516
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.128	0.05	1514
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.119	0.05	1507
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.104	0.05	1456
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.088	0.05	1492
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.114	0.05	1462
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.122	0.05	1520
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.125	0.05	1514
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.117	0.05	1505
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.117	0.05	1468
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.093	0.05	1503
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.112	0.05	1460
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.093	0.05	1608
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.095	0.05	1596
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.102	0.05	1467
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.109	0.05	1473
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.085	0.05	1516
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.055	0.05	1644
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.056	0.05	1515
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.106	0.05	1483
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.024	0.05	1565
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.061	0.05	1497
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.112	0.05	1463
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.049	0.05	1540
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.106	0.05	1515
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.063	0.05	1549
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.1	0.05	1506

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	I	X-RAY DIFFRACTION	Local ncs	0.07587	0.05009
1	2	M	X-RAY DIFFRACTION	Local ncs	0.07587	0.05009
2	3	I	X-RAY DIFFRACTION	Local ncs	0.07276	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07276	0.05009
3	5	I	X-RAY DIFFRACTION	Local ncs	0.05764	0.05009
3	6	B	X-RAY DIFFRACTION	Local ncs	0.05764	0.05009
4	7	M	X-RAY DIFFRACTION	Local ncs	0.07097	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07097	0.05009
5	9	M	X-RAY DIFFRACTION	Local ncs	0.07503	0.05009
5	10	B	X-RAY DIFFRACTION	Local ncs	0.07503	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08049	0.05009
6	12	B	X-RAY DIFFRACTION	Local ncs	0.08049	0.05009
7	13	O	X-RAY DIFFRACTION	Local ncs	0.0835	0.05009
7	14	E	X-RAY DIFFRACTION	Local ncs	0.0835	0.05009
8	15	O	X-RAY DIFFRACTION	Local ncs	0.11805	0.05009
8	16	F	X-RAY DIFFRACTION	Local ncs	0.11805	0.05009
9	17	O	X-RAY DIFFRACTION	Local ncs	0.12794	0.05008
9	18	J	X-RAY DIFFRACTION	Local ncs	0.12794	0.05008
10	19	O	X-RAY DIFFRACTION	Local ncs	0.11933	0.05007
10	20	N	X-RAY DIFFRACTION	Local ncs	0.11933	0.05007
11	21	O	X-RAY DIFFRACTION	Local ncs	0.10441	0.05008
11	22	C	X-RAY DIFFRACTION	Local ncs	0.10441	0.05008
12	23	O	X-RAY DIFFRACTION	Local ncs	0.08788	0.05009
12	24	K	X-RAY DIFFRACTION	Local ncs	0.08788	0.05009
13	25	O	X-RAY DIFFRACTION	Local ncs	0.11382	0.05008
13	26	D	X-RAY DIFFRACTION	Local ncs	0.11382	0.05008
14	27	E	X-RAY DIFFRACTION	Local ncs	0.12155	0.05009
14	28	F	X-RAY DIFFRACTION	Local ncs	0.12155	0.05009
15	29	E	X-RAY DIFFRACTION	Local ncs	0.12548	0.05008
15	30	J	X-RAY DIFFRACTION	Local ncs	0.12548	0.05008
16	31	E	X-RAY DIFFRACTION	Local ncs	0.11681	0.05008
16	32	N	X-RAY DIFFRACTION	Local ncs	0.11681	0.05008
17	33	E	X-RAY DIFFRACTION	Local ncs	0.11691	0.05008
17	34	C	X-RAY DIFFRACTION	Local ncs	0.11691	0.05008
18	35	E	X-RAY DIFFRACTION	Local ncs	0.09269	0.0501
18	36	K	X-RAY DIFFRACTION	Local ncs	0.09269	0.0501
19	37	E	X-RAY DIFFRACTION	Local ncs	0.11181	0.05008
19	38	D	X-RAY DIFFRACTION	Local ncs	0.11181	0.05008
20	39	F	X-RAY DIFFRACTION	Local ncs	0.09316	0.05009
20	40	J	X-RAY DIFFRACTION	Local ncs	0.09316	0.05009
21	41	F	X-RAY DIFFRACTION	Local ncs	0.09484	0.05009
21	42	N	X-RAY DIFFRACTION	Local ncs	0.09484	0.05009
22	43	F	X-RAY DIFFRACTION	Local ncs	0.10234	0.05009
22	44	C	X-RAY DIFFRACTION	Local ncs	0.10234	0.05009
23	45	F	X-RAY DIFFRACTION	Local ncs	0.10888	0.05009
23	46	K	X-RAY DIFFRACTION	Local ncs	0.10888	0.05009
24	47	F	X-RAY DIFFRACTION	Local ncs	0.0853	0.05009
24	48	D	X-RAY DIFFRACTION	Local ncs	0.0853	0.05009
25	49	J	X-RAY DIFFRACTION	Local ncs	0.05458	0.05009
25	50	N	X-RAY DIFFRACTION	Local ncs	0.05458	0.05009
26	51	J	X-RAY DIFFRACTION	Local ncs	0.0555	0.05009
26	52	C	X-RAY DIFFRACTION	Local ncs	0.0555	0.05009
27	53	J	X-RAY DIFFRACTION	Local ncs	0.1065	0.05009
27	54	K	X-RAY DIFFRACTION	Local ncs	0.1065	0.05009
28	55	J	X-RAY DIFFRACTION	Local ncs	0.02413	0.0501
28	56	D	X-RAY DIFFRACTION	Local ncs	0.02413	0.0501
29	57	N	X-RAY DIFFRACTION	Local ncs	0.06095	0.05009
29	58	C	X-RAY DIFFRACTION	Local ncs	0.06095	0.05009
30	59	N	X-RAY DIFFRACTION	Local ncs	0.11205	0.05008
30	60	K	X-RAY DIFFRACTION	Local ncs	0.11205	0.05008
31	61	N	X-RAY DIFFRACTION	Local ncs	0.04884	0.05009
31	62	D	X-RAY DIFFRACTION	Local ncs	0.04884	0.05009
32	63	C	X-RAY DIFFRACTION	Local ncs	0.10646	0.05008
32	64	K	X-RAY DIFFRACTION	Local ncs	0.10646	0.05008
33	65	C	X-RAY DIFFRACTION	Local ncs	0.06259	0.05009
33	66	D	X-RAY DIFFRACTION	Local ncs	0.06259	0.05009
34	67	K	X-RAY DIFFRACTION	Local ncs	0.1004	0.05008
34	68	D	X-RAY DIFFRACTION	Local ncs	0.1004	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.45-2.514	0.381	194	0.318	3950	X-RAY DIFFRACTION	99.7593
2.514-2.582	0.354	210	0.313	3839	X-RAY DIFFRACTION	99.8028
2.582-2.657	0.344	193	0.293	3714	X-RAY DIFFRACTION	99.5668
2.657-2.739	0.319	187	0.272	3618	X-RAY DIFFRACTION	99.7902
2.739-2.829	0.312	187	0.253	3502	X-RAY DIFFRACTION	99.4608
2.829-2.928	0.271	172	0.241	3429	X-RAY DIFFRACTION	99.3379
2.928-3.038	0.285	191	0.238	3258	X-RAY DIFFRACTION	99.6821
3.038-3.162	0.276	168	0.235	3157	X-RAY DIFFRACTION	99.8199
3.162-3.303	0.275	152	0.218	3044	X-RAY DIFFRACTION	99.875
3.303-3.464	0.257	128	0.218	2934	X-RAY DIFFRACTION	99.9347
3.464-3.651	0.239	130	0.209	2789	X-RAY DIFFRACTION	99.829
3.651-3.872	0.213	155	0.189	2617	X-RAY DIFFRACTION	99.8919
3.872-4.139	0.162	123	0.161	2454	X-RAY DIFFRACTION	99.652
4.139-4.47	0.172	110	0.142	2328	X-RAY DIFFRACTION	99.7953
4.47-4.895	0.165	112	0.138	2096	X-RAY DIFFRACTION	99.7741
4.895-5.472	0.196	92	0.156	1926	X-RAY DIFFRACTION	99.8022
5.472-6.315	0.213	100	0.188	1698	X-RAY DIFFRACTION	99.778
6.315-7.726	0.156	55	0.154	1468	X-RAY DIFFRACTION	99.4125
7.726-10	0.142	65	0.132	1114	X-RAY DIFFRACTION	99.4098
8-10	0.305	21	0.248	638	X-RAY DIFFRACTION	96.6276

-
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