PDB-7cj9: Crystal structure of N-terminal His-tagged D-allulose 3-epimerase...

ID or keywords:

Entry

Database: PDB / ID: 7cj9

Title

Crystal structure of N-terminal His-tagged D-allulose 3-epimerase from Methylomonas sp. with additional C-terminal residues

Components

Epimerase

Keywords

ISOMERASE / Epimerase / TIM barrel

Function / homology

Function and homology information

D-tagatose 3-epimerase / isomerase activity / metal ion binding
Similarity search - Function

Biological species

Methylomonas sp. DH-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

Yoshida, H. / Yoshihara, A. / Kamitori, S.

Citation

Journal: Febs Open Bio / Year: 2021
Title: Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp.
Authors: Yoshida, H. / Yoshihara, A. / Kato, S. / Mochizuki, S. / Akimitsu, K. / Izumori, K. / Kamitori, S.

History

Deposition	Jul 9, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 9, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	7cj9.cif.gz	983.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7cj9.ent.gz	813.7 KB	Display	PDB format
PDBx/mmJSON format	7cj9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/7cj9 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cj9	HTTPS FTP

-
Related structure data

Related structure data	7cj4C 7cj5C 7cj6C 7cj7C 7cj8C 5zfsS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7cj4-d 7cj6-d 7cj8-2 4tz0-d 7cj7-d 4b20-3 4ndq-d 1zbq-2 3k6k-1 7cj8-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: Epimerase

B: Epimerase

C: Epimerase

D: Epimerase

E: Epimerase

F: Epimerase

G: Epimerase

H: Epimerase

hetero molecules

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

1

A: Epimerase

B: Epimerase

hetero molecules

defined by author
69.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Epimerase

D: Epimerase

hetero molecules

defined by author
70.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Epimerase

F: Epimerase

hetero molecules

defined by author
70.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Epimerase

H: Epimerase

hetero molecules

defined by author
69.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.430, 92.770, 93.780
Angle α, β, γ (deg.)	87.670, 98.640, 115.600
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

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	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	1	MET	MET	ARG	ARG	B	B	1 - 285	22 - 306
1	2	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	2	MET	MET	ARG	ARG	C	C	1 - 285	22 - 306
1	3	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	3	MET	MET	ARG	ARG	D	D	1 - 285	22 - 306
1	4	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	4	MET	MET	ARG	ARG	E	E	1 - 285	22 - 306
1	5	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	5	MET	MET	ARG	ARG	F	F	1 - 285	22 - 306
1	6	MET	MET	LEU	LEU	A	A	1 - 286	22 - 307
2	6	MET	MET	LEU	LEU	G	G	1 - 286	22 - 307
1	7	MET	MET	ARG	ARG	A	A	1 - 285	22 - 306
2	7	MET	MET	ARG	ARG	H	H	1 - 285	22 - 306
1	8	MET	MET	ARG	ARG	B	B	1 - 285	22 - 306
2	8	MET	MET	ARG	ARG	C	C	1 - 285	22 - 306
1	9	MET	MET	ALA	ALA	B	B	1 - 288	22 - 309
2	9	MET	MET	ALA	ALA	D	D	1 - 288	22 - 309
1	10	MET	MET	THR	THR	B	B	1 - 287	22 - 308
2	10	MET	MET	THR	THR	E	E	1 - 287	22 - 308
1	11	MET	MET	ARG	ARG	B	B	1 - 285	22 - 306
2	11	MET	MET	ARG	ARG	F	F	1 - 285	22 - 306
1	12	MET	MET	ARG	ARG	B	B	1 - 285	22 - 306
2	12	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
1	13	MET	MET	LEU	LEU	B	B	1 - 286	22 - 307
2	13	MET	MET	LEU	LEU	H	H	1 - 286	22 - 307
1	14	MET	MET	ARG	ARG	C	C	1 - 285	22 - 306
2	14	MET	MET	ARG	ARG	D	D	1 - 285	22 - 306
1	15	MET	MET	ARG	ARG	C	C	1 - 285	22 - 306
2	15	MET	MET	ARG	ARG	E	E	1 - 285	22 - 306
1	16	SER	SER	ARG	ARG	C	C	0 - 285	21 - 306
2	16	SER	SER	ARG	ARG	F	F	0 - 285	21 - 306
1	17	MET	MET	ARG	ARG	C	C	1 - 285	22 - 306
2	17	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
1	18	SER	SER	ARG	ARG	C	C	0 - 285	21 - 306
2	18	SER	SER	ARG	ARG	H	H	0 - 285	21 - 306
1	19	MET	MET	THR	THR	D	D	1 - 287	22 - 308
2	19	MET	MET	THR	THR	E	E	1 - 287	22 - 308
1	20	MET	MET	ARG	ARG	D	D	1 - 285	22 - 306
2	20	MET	MET	ARG	ARG	F	F	1 - 285	22 - 306
1	21	MET	MET	ARG	ARG	D	D	1 - 285	22 - 306
2	21	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
1	22	MET	MET	LEU	LEU	D	D	1 - 286	22 - 307
2	22	MET	MET	LEU	LEU	H	H	1 - 286	22 - 307
1	23	MET	MET	ARG	ARG	E	E	1 - 285	22 - 306
2	23	MET	MET	ARG	ARG	F	F	1 - 285	22 - 306
1	24	MET	MET	ARG	ARG	E	E	1 - 285	22 - 306
2	24	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
1	25	MET	MET	LEU	LEU	E	E	1 - 286	22 - 307
2	25	MET	MET	LEU	LEU	H	H	1 - 286	22 - 307
1	26	MET	MET	ARG	ARG	F	F	1 - 285	22 - 306
2	26	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
1	27	SER	SER	ARG	ARG	F	F	0 - 285	21 - 306
2	27	SER	SER	ARG	ARG	H	H	0 - 285	21 - 306
1	28	MET	MET	ARG	ARG	G	G	1 - 285	22 - 306
2	28	MET	MET	ARG	ARG	H	H	1 - 285	22 - 306

NCS ensembles :
NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.95462, -0.023828, 0.29687), (0.008873, -0.998627, -0.051624), (0.297693, -0.046647, 0.953521)	25.323271, -21.367661, -4.55548
3	given	(1), (1), (1)
4	given	(0.999144, -0.003908, 0.041177), (-0.001639, 0.991006, 0.13381), (-0.041329, -0.133763, 0.990151)	19.46669, 40.377548, -8.94221
5	given	(1), (1), (1)
6	given	(-0.95871, -0.018958, 0.283753), (-0.041209, -0.977983, -0.204573), (0.281384, -0.20782, 0.936821)	5.4287, -61.413231, -10.3799
7	given	(1), (1), (1)
8	given	(-0.954853, 0.027732, -0.295782), (-0.031897, 0.980308, 0.194883), (0.295362, 0.195519, -0.935165)	42.751301, -74.536667, 22.61133
9	given	(1), (1), (1)
10	given	(0.99972, 0.004147, -0.023303), (0.001274, -0.992535, -0.121955), (-0.023634, 0.121891, -0.992262)	-5.66213, 51.21505, 35.37215
11	given	(1), (1), (1)
12	given	(-0.958035, 0.026518, -0.285423), (0.009012, 0.998006, 0.062474), (0.28651, 0.05728, -0.956363)	62.73177, -29.74118, 29.556511
13	given	(1), (1), (1)
14	given	(0.999964, -0.002327, -0.008217), (-0.002421, -0.999932, -0.011408), (-0.008189, 0.011427, -0.999901)	-25.751551, 6.0127, 43.813992
15	given	(1), (1), (1)
16	given	(-0.966195, -0.026986, 0.256397), (-0.020525, -0.983299, -0.180839), (0.256995, -0.179988, 0.949504)	4.84305, -61.323372, -9.12161
17	given	(1), (1), (1)
18	given	(0.998596, -0.05264, 0.005889), (0.051109, 0.986759, 0.15393), (-0.013914, -0.153413, 0.988064)	16.888491, 40.729389, -9.40338
19	given	(1), (1), (1)
20	given	(0.999157, 0.040609, 0.005932), (0.041041, -0.988696, -0.144211), (9.0E-6, 0.144333, -0.989529)	-9.04629, 51.41193, 33.793961
21	given	(1), (1), (1)
22	given	(-0.961418, 0.023199, -0.274113), (-0.024323, 0.985367, 0.168703), (0.274015, 0.168862, -0.946785)	42.118469, -73.609421, 25.118839
23	given	(1), (1), (1)
24	given	(0.999935, 0.000877, -0.011376), (0.000753, -0.99994, -0.010926), (-0.011385, 0.010917, -0.999876)	-25.65299, 5.86078, 44.050499
25	given	(1), (1), (1)
26	given	(-0.957102, -0.003478, -0.289732), (-0.021281, 0.998071, 0.058317), (0.28897, 0.061981, -0.95533)	63.39275, -28.381029, 29.551279
27	given	(1), (1), (1)
28	given	(-0.96954, -0.008473, 0.244787), (-0.074751, -0.941486, -0.328658), (0.233248, -0.336946, 0.912175)	-13.78317, -100.637733, -15.59596
29	given	(1), (1), (1)
30	given	(-0.966255, 0.017809, -0.256972), (-0.06743, 0.945332, 0.319062), (0.248606, 0.325623, -0.912231)	22.15592, -118.185081, 16.85638
31	given	(1), (1), (1)
32	given	(0.999834, 0.001085, 0.018213), (0.000872, -0.999931, 0.011696), (0.018224, -0.011678, -0.999766)	-26.98167, 4.917, 44.272968
33	given	(1), (1), (1)
34	given	(-0.969124, 0.022355, -0.245557), (-0.02567, 0.981322, 0.19065), (0.245233, 0.191067, -0.950449)	41.749561, -74.794884, 30.53834
35	given	(1), (1), (1)
36	given	(0.999442, -0.000826, 0.033381), (-0.004893, -0.992528, 0.121921), (0.033031, -0.122017, -0.991978)	-47.313591, -40.921669, 45.763069
37	given	(1), (1), (1)
38	given	(0.999855, -0.011756, 0.012358), (-0.01187, -0.999888, 0.009158), (0.012249, -0.009303, -0.999882)	-25.97295, 5.27228, 44.168831
39	given	(1), (1), (1)
40	given	(-0.965179, 0.070913, -0.251797), (-0.015556, 0.945294, 0.32585), (0.261129, 0.31842, -0.911274)	18.876841, -119.443977, 16.674841
41	given	(1), (1), (1)
42	given	(0.998736, -0.050214, 0.002255), (-0.05002, -0.988467, 0.142934), (-0.004948, -0.142866, -0.98973)	-45.025669, -40.36335, 47.1754
43	given	(1), (1), (1)
44	given	(-0.960936, 0.046437, -0.272846), (-0.015076, 0.975578, 0.219137), (0.276359, 0.21469, -0.936768)	42.357658, -76.609154, 28.136009
45	given	(1), (1), (1)
46	given	(-0.96167, 0.063515, -0.266753), (0.024447, -0.949071, -0.314112), (-0.273118, -0.308593, 0.91114)	45.987202, 124.425797, 26.886259
47	given	(1), (1), (1)
48	given	(0.999123, -0.040199, -0.011697), (0.03828, 0.990301, -0.13356), (0.016953, 0.132995, 0.990972)	-18.467779, 45.821602, -3.66125
49	given	(1), (1), (1)
50	given	(-0.957239, 0.037273, -0.286888), (0.023976, -0.978033, -0.207066), (-0.288304, -0.20509, 0.935318)	69.097481, 81.208946, 16.12393
51	given	(1), (1), (1)
52	given	(-0.964464, 0.026803, -0.262852), (0.021777, -0.983392, -0.180181), (-0.263316, -0.179502, 0.947863)	68.402733, 79.959267, 14.07832
53	given	(1), (1), (1)
54	given	(0.999879, -0.004202, 0.014968), (0.005835, 0.993833, -0.110737), (-0.014411, 0.110811, 0.993737)	-20.32126, 45.809719, -2.40809
55	given	(1), (1), (1)
56	given	(-0.960336, -0.003526, -0.278823), (0.023702, -0.997333, -0.069024), (-0.277836, -0.072895, 0.957859)	89.179527, 34.158669, 13.86131

-
Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein	Epimerase Mass: 34485.852 Da / Num. of mol.: 8 / Mutation: Y9T, Y37F, Y286L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylomonas sp. DH-1 (bacteria) / Gene: AYM39_05640 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A172U6X0
#3: Sugar	ChemComp-FUD / D-fructose Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#1: Protein

Epimerase

Mass: 34485.852 Da / Num. of mol.: 8 / Mutation: Y9T, Y37F, Y286L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methylomonas sp. DH-1 (bacteria) / Gene: AYM39_05640 / Plasmid: pET15b / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A172U6X0

#3: Sugar

ChemComp-FUD / D-fructose

Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 4 types, 2181 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2158 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ethylene glycol, HEPES, PEG8000

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-5A / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.58→45.71 Å / Num. obs: 311350 / % possible obs: 94 % / Redundancy: 3.472 % / B_iso Wilson estimate: 25.715 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.034 / R_rim(I) all: 0.041 / Χ²: 1 / Net I/σ(I): 22.43 / Num. measured all: 1081104 / Scaling rejects: 13660

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.58-1.62	3.63	0.457	2.82	84112	24458	23169	0.83	0.538	94.7
1.62-1.67	3.62	0.368	3.55	81998	23846	22650	0.888	0.432	95
1.67-1.71	3.564	0.294	4.33	78993	23271	22162	0.92	0.347	95.2
1.71-1.77	3.493	0.232	5.34	75191	22553	21529	0.944	0.274	95.5
1.77-1.82	3.358	0.185	6.46	70459	21904	20980	0.961	0.221	95.8
1.82-1.89	3.377	0.176	6.74	67231	21127	19909	0.973	0.211	94.2
1.89-1.96	3.295	0.082	15.1	51511	20452	15634	0.996	0.099	76.4
1.96-2.04	3.605	0.093	13.16	68097	19622	18889	0.991	0.109	96.3
2.04-2.13	3.563	0.072	16.69	64757	18850	18175	0.994	0.085	96.4
2.13-2.23	3.34	0.061	19.04	55150	18037	16514	0.994	0.074	91.6
2.23-2.36	3.166	0.042	26.58	45511	17030	14373	0.997	0.052	84.4
2.36-2.5	3.482	0.037	29.13	54816	16247	15743	0.998	0.044	96.9
2.5-2.67	3.639	0.032	35.34	54077	15216	14859	0.999	0.037	97.7
2.67-2.88	3.56	0.026	41.95	49271	14134	13842	0.999	0.031	97.9
2.88-3.16	3.297	0.022	48.56	41748	13008	12662	0.999	0.027	97.3
3.16-3.53	3.25	0.017	57.05	37366	11789	11497	0.999	0.02	97.5
3.53-4.08	3.479	0.016	66.19	33968	10412	9764	0.999	0.019	93.8
4.08-5	3.575	0.012	73.47	30878	8740	8637	1	0.014	98.8
5-7.07	3.315	0.013	68.38	22275	6780	6719	1	0.016	99.1
7.07-45.71	3.759	0.01	81.33	13695	3706	3643	1	0.012	98.3

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs

Resolution: 1.58→45.71 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.921 / SU B: 5.007 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2269	15718	5 %	RANDOM
R_work	0.1767	-	-	-
obs	0.1792	295623	94.02 %	-

Solvent computation

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

Displacement parameters

B_iso max: 83.48 Å² / B_iso mean: 20.931 Å² / B_iso min: 11.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0.02 Å²	-0.36 Å²
2-	-	0.15 Å²	0.21 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: final / Resolution: 1.58→45.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17677	0	252	2158	20087
B_iso mean	-	-	29.79	34.1	-
Num. residues	-	-	-	-	2302

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	18329
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	16972
X-RAY DIFFRACTION	r_angle_refined_deg	1.252	1.643	24841
X-RAY DIFFRACTION	r_angle_other_deg	1.336	1.595	39219
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.347	5	2312
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.489	22.157	955
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.976	15	2934
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.848	15	121
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	2380
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	20741
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	3950
X-RAY DIFFRACTION	r_rigid_bond_restr	4.695	3	35301

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2211	TIGHT POSITIONAL	0.34	0.13
1	A	2196	TIGHT POSITIONAL	0.4	0.13
1	A	2196	TIGHT POSITIONAL	0.19	0.13
1	A	2204	TIGHT POSITIONAL	0.3	0.13
1	A	2202	TIGHT POSITIONAL	0.43	0.13
1	A	2202	TIGHT POSITIONAL	0.35	0.13
1	A	2208	TIGHT POSITIONAL	0.28	0.13
1	A	2202	TIGHT POSITIONAL	0.4	0.13
1	A	2208	TIGHT POSITIONAL	0.4	0.13
1	A	2211	TIGHT POSITIONAL	0.31	0.13
1	A	2199	TIGHT THERMAL	10.35	1.32
2	A	2196	TIGHT POSITIONAL	0.4	0.13
2	A	2196	TIGHT POSITIONAL	0.29	0.13
2	A	2204	TIGHT POSITIONAL	0.26	0.13
2	A	2204	TIGHT POSITIONAL	0.29	0.13
2	A	2204	TIGHT POSITIONAL	0.35	0.13
2	A	2212	TIGHT POSITIONAL	0.37	0.13
2	A	2190	TIGHT POSITIONAL	0.4	0.13
2	A	2196	TIGHT POSITIONAL	0.39	0.13
2	A	2190	TIGHT POSITIONAL	0.3	0.13
2	A	2199	TIGHT THERMAL	3.9	1.32
3	A	2199	TIGHT THERMAL	11.56	1.32
4	A	2199	TIGHT THERMAL	5.71	1.32
5	A	2199	TIGHT THERMAL	10.06	1.32
6	A	2207	TIGHT THERMAL	5.65	1.32
7	A	2199	TIGHT THERMAL	9.69	1.32
8	B	2196	TIGHT THERMAL	10.39	1.32
9	B	2216	TIGHT THERMAL	4.57	1.32
10	B	2211	TIGHT THERMAL	9.07	1.32
11	B	2196	TIGHT THERMAL	5.94	1.32
12	B	2196	TIGHT THERMAL	10.54	1.32
13	B	2204	TIGHT THERMAL	5.54	1.32
14	C	2202	TIGHT THERMAL	11.69	1.32
15	C	2202	TIGHT THERMAL	5.78	1.32
16	C	2208	TIGHT THERMAL	9.81	1.32
17	C	2202	TIGHT THERMAL	5.95	1.32
18	C	2208	TIGHT THERMAL	10	1.32
19	D	2211	TIGHT THERMAL	10.14	1.32
20	D	2196	TIGHT THERMAL	6.7	1.32
21	D	2196	TIGHT THERMAL	12.22	1.32
22	D	2204	TIGHT THERMAL	6.22	1.32
23	E	2204	TIGHT THERMAL	9.16	1.32
24	E	2204	TIGHT THERMAL	5	1.32
25	E	2212	TIGHT THERMAL	8.9	1.32
26	F	2190	TIGHT THERMAL	11.3	1.32
27	F	2196	TIGHT THERMAL	4.12	1.32
28	G	2190	TIGHT THERMAL	10.94	1.32

LS refinement shell

Resolution: 1.58→1.621 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	1191	-
R_work	0.184	21946	-
all	-	23137	-
obs	-	-	94.66 %

-
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

-
Protein / Sugars , 2 types, 16 molecules ABCDEFGH

-
Non-polymers , 4 types, 2181 molecules

-
Details

-
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

-Protein / Sugars , 2 types, 16 molecules ABCDEFGH

-Non-polymers , 4 types, 2181 molecules

-Details

-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

-
Protein / Sugars , 2 types, 16 molecules ABCDEFGH

-
Non-polymers , 4 types, 2181 molecules

-
Details

-
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