PDB-7y0x: Orf1-glycine complex

ID or keywords:

Entry

Database: PDB / ID: 7y0x

Title

Orf1-glycine complex

Components

N-formimidoyl fortimicin A synthase

Keywords

OXIDOREDUCTASE / glycine complex cysteine-adduct

Function / homology

FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / nucleotide binding / cytoplasm / FLAVIN-ADENINE DINUCLEOTIDE / GLYCINE / Chem-I55 / N-formimidoyl fortimicin A synthase

Function and homology information

Biological species

Streptomyces luteocolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Wang, Y.L. / Li, T.L.

Funding support

Taiwan, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Authors: Wang, Y.L. / Chang, C.Y. / Hsu, N.S. / Lo, I.W. / Lin, K.H. / Chen, C.L. / Chang, C.F. / Wang, Z.C. / Ogasawara, Y. / Dairi, T. / Maruyama, C. / Hamano, Y. / Li, T.L.

History

Deposition	Jun 6, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7y0x.cif.gz	784.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7y0x.ent.gz	626.8 KB	Display	PDB format
PDBx/mmJSON format	7y0x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7y0x_validation.pdf.gz	7.6 MB	Display	wwPDB validaton report
Full document	7y0x_full_validation.pdf.gz	7.6 MB	Display
Data in XML	7y0x_validation.xml.gz	143.8 KB	Display
Data in CIF	7y0x_validation.cif.gz	200.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/7y0x ftp://data.pdbj.org/pub/pdb/validation_reports/y0/7y0x	HTTPS FTP

-
Related structure data

Related structure data	7xqaSC 7xx0C 7xxcC 7xxdC 7xxmC 7xxpC 7xxrC 7xyeC 7xylC 7ypuC 7ypvC 8griC 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
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: N-formimidoyl fortimicin A synthase

B: N-formimidoyl fortimicin A synthase

C: N-formimidoyl fortimicin A synthase

D: N-formimidoyl fortimicin A synthase

E: N-formimidoyl fortimicin A synthase

F: N-formimidoyl fortimicin A synthase

G: N-formimidoyl fortimicin A synthase

H: N-formimidoyl fortimicin A synthase

hetero molecules

446 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-formimidoyl fortimicin A synthase

B: N-formimidoyl fortimicin A synthase

C: N-formimidoyl fortimicin A synthase

D: N-formimidoyl fortimicin A synthase

hetero molecules

defined by author&software
Evidence: gel filtration
223 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: N-formimidoyl fortimicin A synthase

F: N-formimidoyl fortimicin A synthase

G: N-formimidoyl fortimicin A synthase

H: N-formimidoyl fortimicin A synthase

hetero molecules

defined by author&software
223 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.425, 107.225, 135.159
Angle α, β, γ (deg.)	90.054, 90.040, 83.684
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	THR	THR	TRP	TRP	A	A	11 - 490	28 - 507
2	2	1	THR	THR	TRP	TRP	B	B	11 - 490	28 - 507
3	3	2	THR	THR	TRP	TRP	A	A	11 - 490	28 - 507
4	4	2	THR	THR	TRP	TRP	C	C	11 - 490	28 - 507
5	5	3	VAL	VAL	TRP	TRP	A	A	13 - 490	30 - 507
6	6	3	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
7	7	4	THR	THR	TRP	TRP	A	A	11 - 490	28 - 507
8	8	4	THR	THR	TRP	TRP	E	E	11 - 490	28 - 507
9	9	5	THR	THR	TRP	TRP	A	A	11 - 490	28 - 507
10	10	5	THR	THR	TRP	TRP	F	F	11 - 490	28 - 507
11	11	6	THR	THR	HIS	HIS	A	A	11 - 491	28 - 508
12	12	6	THR	THR	HIS	HIS	G	G	11 - 491	28 - 508
13	13	7	VAL	VAL	TRP	TRP	A	A	13 - 490	30 - 507
14	14	7	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507
15	15	8	GLN	GLN	HIS	HIS	B	B	10 - 491	27 - 508
16	16	8	GLN	GLN	HIS	HIS	C	C	10 - 491	27 - 508
17	17	9	VAL	VAL	TRP	TRP	B	B	13 - 490	30 - 507
18	18	9	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
19	19	10	GLN	GLN	HIS	HIS	B	B	10 - 491	27 - 508
20	20	10	GLN	GLN	HIS	HIS	E	E	10 - 491	27 - 508
21	21	11	GLN	GLN	HIS	HIS	B	B	10 - 491	27 - 508
22	22	11	GLN	GLN	HIS	HIS	F	F	10 - 491	27 - 508
23	23	12	THR	THR	TRP	TRP	B	B	11 - 490	28 - 507
24	24	12	THR	THR	TRP	TRP	G	G	11 - 490	28 - 507
25	25	13	VAL	VAL	TRP	TRP	B	B	13 - 490	30 - 507
26	26	13	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507
27	27	14	VAL	VAL	TRP	TRP	C	C	13 - 490	30 - 507
28	28	14	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
29	29	15	GLN	GLN	HIS	HIS	C	C	10 - 491	27 - 508
30	30	15	GLN	GLN	HIS	HIS	E	E	10 - 491	27 - 508
31	31	16	GLN	GLN	HIS	HIS	C	C	10 - 491	27 - 508
32	32	16	GLN	GLN	HIS	HIS	F	F	10 - 491	27 - 508
33	33	17	THR	THR	TRP	TRP	C	C	11 - 490	28 - 507
34	34	17	THR	THR	TRP	TRP	G	G	11 - 490	28 - 507
35	35	18	VAL	VAL	TRP	TRP	C	C	13 - 490	30 - 507
36	36	18	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507
37	37	19	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
38	38	19	VAL	VAL	TRP	TRP	E	E	13 - 490	30 - 507
39	39	20	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
40	40	20	VAL	VAL	TRP	TRP	F	F	13 - 490	30 - 507
41	41	21	VAL	VAL	TRP	TRP	D	D	13 - 490	30 - 507
42	42	21	VAL	VAL	TRP	TRP	G	G	13 - 490	30 - 507
43	43	22	VAL	VAL	HIS	HIS	D	D	13 - 491	30 - 508
44	44	22	VAL	VAL	HIS	HIS	H	H	13 - 491	30 - 508
45	45	23	GLN	GLN	HIS	HIS	E	E	10 - 491	27 - 508
46	46	23	GLN	GLN	HIS	HIS	F	F	10 - 491	27 - 508
47	47	24	THR	THR	TRP	TRP	E	E	11 - 490	28 - 507
48	48	24	THR	THR	TRP	TRP	G	G	11 - 490	28 - 507
49	49	25	VAL	VAL	TRP	TRP	E	E	13 - 490	30 - 507
50	50	25	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507
51	51	26	THR	THR	TRP	TRP	F	F	11 - 490	28 - 507
52	52	26	THR	THR	TRP	TRP	G	G	11 - 490	28 - 507
53	53	27	VAL	VAL	TRP	TRP	F	F	13 - 490	30 - 507
54	54	27	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507
55	55	28	VAL	VAL	TRP	TRP	G	G	13 - 490	30 - 507
56	56	28	VAL	VAL	TRP	TRP	H	H	13 - 490	30 - 507

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

#1: Protein	N-formimidoyl fortimicin A synthase Mass: 54424.238 Da / Num. of mol.: 8 / Mutation: F316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces luteocolor (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125SZC1
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-I55 / [(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl] carbamate Mass: 431.401 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₅N₇O₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₅NO₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1395 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000

-
Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.05→30 Å / Num. obs: 354721 / % possible obs: 97.4 % / Redundancy: 4.2 % / R_merge(I) obs: 0.057 / R_pim(I) all: 0.031 / R_rim(I) all: 0.065 / Net I/σ(I): 28
Reflection shell	Resolution: 2.05→2.12 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.608 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 33161 / R_pim(I) all: 0.331 / R_rim(I) all: 0.693 / % possible all: 91.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XQA

7xqa

Resolution: 2.05→27.739 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.938 / WR_factor R_free: 0.196 / WR_factor R_work: 0.182 / SU B: 3.719 / SU ML: 0.1 / Average fsc free: 0.9227 / Average fsc work: 0.9281 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2145	17716	5.02 %
R_work	0.1986	335201	-
all	0.199	-	-
obs	-	352917	97.441 %

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: 29.249 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.033 Å²	-0.029 Å²	-0.095 Å²
2-	-	0.055 Å²	0.089 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→27.739 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29118	0	704	1395	31217

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	30526
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	28356
X-RAY DIFFRACTION	r_angle_refined_deg	1.442	1.642	41702
X-RAY DIFFRACTION	r_angle_other_deg	1.307	1.575	65096
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.591	5	3840
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.124	20.306	1634
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.954	15	4532
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.675	15	280
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	3974
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	34920
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6888
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	5551
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	25583
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	14626
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	13760
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	1349
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.145	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	2.098	2.91	15408
X-RAY DIFFRACTION	r_mcbond_other	2.097	2.91	15406
X-RAY DIFFRACTION	r_mcangle_it	3.15	4.355	19232
X-RAY DIFFRACTION	r_mcangle_other	3.15	4.355	19232
X-RAY DIFFRACTION	r_scbond_it	2.874	3.3	15118
X-RAY DIFFRACTION	r_scbond_other	2.874	3.3	15118
X-RAY DIFFRACTION	r_scangle_it	4.584	4.804	22470
X-RAY DIFFRACTION	r_scangle_other	4.584	4.804	22470
X-RAY DIFFRACTION	r_lrange_it	6.117	34.096	32939
X-RAY DIFFRACTION	r_lrange_other	6.086	34.026	32760
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.049	0.05	15083
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.054	0.05	14978
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.049	0.05	14945
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.022	0.05	15333
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.045	0.05	15102
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.056	0.05	15030
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.049	0.05	14930
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.059	0.05	15068
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.051	0.05	14921
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.05	0.05	15156
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.031	0.05	15364
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.051	0.05	14997
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.05	0.05	14919
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.058	0.05	14884
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.056	0.05	15030
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.052	0.05	15104
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.032	0.05	15262
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.056	0.05	14886
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.049	0.05	14956
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.045	0.05	14955
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.054	0.05	14889
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.019	0.05	15262
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.048	0.05	15158
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.051	0.05	14984
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.05	0.05	14941
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.049	0.05	14992
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.045	0.05	14942
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.051	0.05	14897

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	0.04938	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.04938	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05436	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05436	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04874	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.04874	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.02234	0.0501
4	8	E	X-RAY DIFFRACTION	Local ncs	0.02234	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04542	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.04542	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05576	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.05576	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.04924	0.05009
7	14	H	X-RAY DIFFRACTION	Local ncs	0.04924	0.05009
8	15	B	X-RAY DIFFRACTION	Local ncs	0.05868	0.05009
8	16	C	X-RAY DIFFRACTION	Local ncs	0.05868	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.0515	0.05009
9	18	D	X-RAY DIFFRACTION	Local ncs	0.0515	0.05009
10	19	B	X-RAY DIFFRACTION	Local ncs	0.0503	0.05009
10	20	E	X-RAY DIFFRACTION	Local ncs	0.0503	0.05009
11	21	B	X-RAY DIFFRACTION	Local ncs	0.03091	0.0501
11	22	F	X-RAY DIFFRACTION	Local ncs	0.03091	0.0501
12	23	B	X-RAY DIFFRACTION	Local ncs	0.05052	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.05052	0.05009
13	25	B	X-RAY DIFFRACTION	Local ncs	0.04989	0.05009
13	26	H	X-RAY DIFFRACTION	Local ncs	0.04989	0.05009
14	27	C	X-RAY DIFFRACTION	Local ncs	0.05755	0.05009
14	28	D	X-RAY DIFFRACTION	Local ncs	0.05755	0.05009
15	29	C	X-RAY DIFFRACTION	Local ncs	0.05601	0.05009
15	30	E	X-RAY DIFFRACTION	Local ncs	0.05601	0.05009
16	31	C	X-RAY DIFFRACTION	Local ncs	0.0523	0.05009
16	32	F	X-RAY DIFFRACTION	Local ncs	0.0523	0.05009
17	33	C	X-RAY DIFFRACTION	Local ncs	0.03212	0.0501
17	34	G	X-RAY DIFFRACTION	Local ncs	0.03212	0.0501
18	35	C	X-RAY DIFFRACTION	Local ncs	0.05631	0.05009
18	36	H	X-RAY DIFFRACTION	Local ncs	0.05631	0.05009
19	37	D	X-RAY DIFFRACTION	Local ncs	0.04903	0.05009
19	38	E	X-RAY DIFFRACTION	Local ncs	0.04903	0.05009
20	39	D	X-RAY DIFFRACTION	Local ncs	0.04473	0.05009
20	40	F	X-RAY DIFFRACTION	Local ncs	0.04473	0.05009
21	41	D	X-RAY DIFFRACTION	Local ncs	0.05423	0.05009
21	42	G	X-RAY DIFFRACTION	Local ncs	0.05423	0.05009
22	43	D	X-RAY DIFFRACTION	Local ncs	0.01918	0.0501
22	44	H	X-RAY DIFFRACTION	Local ncs	0.01918	0.0501
23	45	E	X-RAY DIFFRACTION	Local ncs	0.04802	0.05009
23	46	F	X-RAY DIFFRACTION	Local ncs	0.04802	0.05009
24	47	E	X-RAY DIFFRACTION	Local ncs	0.0512	0.05009
24	48	G	X-RAY DIFFRACTION	Local ncs	0.0512	0.05009
25	49	E	X-RAY DIFFRACTION	Local ncs	0.04987	0.05009
25	50	H	X-RAY DIFFRACTION	Local ncs	0.04987	0.05009
26	51	F	X-RAY DIFFRACTION	Local ncs	0.04889	0.05009
26	52	G	X-RAY DIFFRACTION	Local ncs	0.04889	0.05009
27	53	F	X-RAY DIFFRACTION	Local ncs	0.04467	0.05009
27	54	H	X-RAY DIFFRACTION	Local ncs	0.04467	0.05009
28	55	G	X-RAY DIFFRACTION	Local ncs	0.05134	0.05009
28	56	H	X-RAY DIFFRACTION	Local ncs	0.05134	0.05009

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 (%)
2.05-2.103	0.28	1202	0.263	22728	X-RAY DIFFRACTION	89.5383
2.103-2.16	0.256	1307	0.245	23893	X-RAY DIFFRACTION	97.1211
2.16-2.223	0.249	1180	0.232	23435	X-RAY DIFFRACTION	97.2387
2.223-2.291	0.249	1036	0.225	22837	X-RAY DIFFRACTION	97.405
2.291-2.365	0.237	1142	0.214	22111	X-RAY DIFFRACTION	97.5296
2.365-2.448	0.239	1175	0.202	21322	X-RAY DIFFRACTION	97.745
2.448-2.54	0.235	1075	0.204	20736	X-RAY DIFFRACTION	97.8994
2.54-2.642	0.238	1113	0.212	19834	X-RAY DIFFRACTION	98.016
2.642-2.759	0.253	1041	0.213	19186	X-RAY DIFFRACTION	98.2084
2.759-2.892	0.238	953	0.21	18290	X-RAY DIFFRACTION	98.3341
2.892-3.047	0.226	912	0.204	17549	X-RAY DIFFRACTION	98.4744
3.047-3.23	0.22	959	0.202	16426	X-RAY DIFFRACTION	98.6439
3.23-3.45	0.221	819	0.205	15663	X-RAY DIFFRACTION	98.7893
3.45-3.723	0.189	773	0.186	14497	X-RAY DIFFRACTION	98.9182
3.723-4.072	0.191	772	0.179	13355	X-RAY DIFFRACTION	99.0882
4.072-4.542	0.164	676	0.16	12112	X-RAY DIFFRACTION	99.0243
4.542-5.224	0.161	597	0.158	10747	X-RAY DIFFRACTION	99.291
5.224-6.351	0.197	443	0.192	9213	X-RAY DIFFRACTION	99.2803
6.351-8.786	0.192	316	0.178	7171	X-RAY DIFFRACTION	99.0475
8.786-27.739	0.203	225	0.187	4095	X-RAY DIFFRACTION	96.364

-
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