PDB-4grs: Crystal structure of a chimeric DAH7PS

ID or keywords:

Entry

Database: PDB / ID: 4grs

Title

Crystal structure of a chimeric DAH7PS

Components

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

Keywords

TRANSFERASE / DAHP / DAHPS / DAH7PS / TIM BARREL / ACT DOMAIN / ALLOSTERIC REGULATION / AROMATIC BIOSYNTHESIS / SHIKIMATE PATHWAY / TRANSFERABLE ALLOSTERY

Function / homology

Function and homology information

3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3 Å

Authors

Cross, P.J. / Allison, T.M. / Dobson, R.C.J. / Jameson, G.B. / Parker, E.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Engineering allosteric control to an unregulated enzyme by transfer of a regulatory domain
Authors: Cross, P.J. / Allison, T.M. / Dobson, R.C.J. / Jameson, G.B. / Parker, E.J.

History

Deposition	Aug 26, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2013	Group: Database references
Revision 1.2	Aug 16, 2017	Group: Data collection / Refinement description / Source and taxonomy Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4grs.cif.gz	510.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4grs.ent.gz	425.2 KB	Display	PDB format
PDBx/mmJSON format	4grs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/4grs ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4grs	HTTPS FTP

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Related structure data

Related structure data	1vr6S 1zco 3pg9 S: Starting model for refinement
Similar structure data	3pg9-2 3pg9-1 1vr6-d 4jyj-1 1szo-6 2ixd-1 1jh7-2 6nxb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#22 - Oct 2001 Photosystem I similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

B: Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

C: Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

D: Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

hetero molecules

149 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	76.901, 130.852, 138.070
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	GLY	GLY	2	A	A	1 - 43	1 - 43
2	1	1	MET	MET	GLY	GLY	2	B	B	1 - 43	1 - 43
3	1	1	MET	MET	GLY	GLY	2	C	C	1 - 43	1 - 43
4	1	1	MET	MET	GLY	GLY	2	D	D	1 - 43	1 - 43
1	1	2	VAL	VAL	PHE	PHE	2	A	A	72 - 130	72 - 130
2	1	2	VAL	VAL	PHE	PHE	2	B	B	72 - 130	72 - 130
3	1	2	VAL	VAL	PHE	PHE	2	C	C	72 - 130	72 - 130
4	1	2	VAL	VAL	PHE	PHE	2	D	D	72 - 130	72 - 130
1	2	2	GLY	GLY	GLY	GLY	1	A	A	141 - 333	141 - 333
2	2	2	GLY	GLY	GLY	GLY	1	B	B	141 - 333	141 - 333
3	2	2	GLY	GLY	GLY	GLY	1	C	C	141 - 333	141 - 333
4	2	2	GLY	GLY	GLY	GLY	1	D	D	141 - 333	141 - 333
1	1	3	LYS	LYS	GLN	GLN	5	A	A	131 - 140	131 - 140
2	1	3	LYS	LYS	GLN	GLN	5	B	B	131 - 140	131 - 140
3	1	3	LYS	LYS	GLN	GLN	5	C	C	131 - 140	131 - 140
4	1	3	LYS	LYS	GLN	GLN	5	D	D	131 - 140	131 - 140
1	1	4	ASP	ASP	VAL	VAL	5	A	A	44 - 49	44 - 49
2	1	4	ASP	ASP	VAL	VAL	5	B	B	44 - 49	44 - 49
3	1	4	ASP	ASP	VAL	VAL	5	C	C	44 - 49	44 - 49
4	1	4	ASP	ASP	VAL	VAL	5	D	D	44 - 49	44 - 49
1	1	5	ALA	ALA	LEU	LEU	2	A	A	50 - 71	50 - 71
2	1	5	ALA	ALA	LEU	LEU	2	B	B	50 - 71	50 - 71
3	1	5	ALA	ALA	LEU	LEU	2	C	C	50 - 71	50 - 71
4	1	5	ALA	ALA	LEU	LEU	2	D	D	50 - 71	50 - 71

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase / DAH7PS Mass: 37114.688 Da / Num. of mol.: 4 / Fragment: UNP residues 1-103, 33-262 Source method: isolated from a genetically manipulated source Details: Fusion protein of Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase Source: (gene. exp.) Thermotoga maritima (bacteria), (gene. exp.) Pyrococcus furiosus (archaea) Strain: MSB8, DSM 3638 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) chaperone 3 References: UniProt: Q9WYH8, UniProt: Q8U0A9, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical	ChemComp-TYR / TYROSINE Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₁NO₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.43 % / Mosaicity: 0.67 °
Crystal grow	Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M sodium chloride, 20%(w/v) polyethylene glycol 6000, 0.1M Tris, 0.02%(w/v) sodium azide, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.953688 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD

Radiation

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

Radiation wavelength

Wavelength: 0.953688 Å / Relative weight: 1

Reflection

Resolution: 3→94.976 Å / Num. all: 27079 / Num. obs: 27079 / % possible obs: 95.5 % / Redundancy: 3 % / R_sym value: 0.101 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) all	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
3-3.16	3	0.702	0.581	1.3	12029	3985	0.389	0.702	0.581	1.7	97.6
3.16-3.35	3	0.44	0.364	2.1	11402	3777	0.243	0.44	0.364	2.8	97.1
3.35-3.59	3	0.277	0.229	3.3	10524	3503	0.153	0.277	0.229	4.6	96.7
3.59-3.87	3	0.195	0.161	4.8	9840	3298	0.108	0.195	0.161	6.3	96.6
3.87-4.24	3	0.127	0.105	7	8928	2990	0.07	0.127	0.105	9.3	96.1
4.24-4.74	2.9	0.091	0.075	9.6	7928	2704	0.051	0.091	0.075	12.3	94.8
4.74-5.48	2.8	0.073	0.06	11.8	6422	2278	0.041	0.073	0.06	13.5	89.8
5.48-6.71	3.1	0.072	0.059	12	6217	2025	0.039	0.072	0.059	15	94.4
6.71-9.49	3.1	0.041	0.034	17.6	5031	1615	0.022	0.041	0.034	23.6	94.4
9.49-37.94	3	0.037	0.03	17.2	2668	904	0.021	0.037	0.03	26.4	91.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VR6

1vr6

Resolution: 3→37.94 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.2285 / WR_factor R_work: 0.1756 / Occupancy max: 1 / Occupancy min: 0.69 / FOM work R set: 0.8323 / SU B: 46.596 / SU ML: 0.395 / SU R Cruickshank DPI: 0.3883 / SU R_free: 0.4835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2481	1350	5 %	RANDOM
R_work	0.192	-	-	-
obs	0.1948	27048	94.54 %	-

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: 242.89 Å² / B_iso mean: 81.971 Å² / B_iso min: 16 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.88 Å²	-0 Å²	0 Å²
2-	-	0.97 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 3→37.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10019	0	52	21	10092

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	10238
X-RAY DIFFRACTION	r_angle_refined_deg	1.143	1.977	13909
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.99	5	1323
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.808	24.33	418
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.9	15	1698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.161	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1648
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	7641

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	109	MEDIUM POSITIONAL	0.07	0.75
1	2	B	109	MEDIUM POSITIONAL	0.08	0.75
1	3	C	109	MEDIUM POSITIONAL	0.07	0.75
1	4	D	109	MEDIUM POSITIONAL	0.08	0.75
1	1	A	172	TIGHT THERMAL	10.66	2
1	2	B	172	TIGHT THERMAL	6.03	2
1	3	C	172	TIGHT THERMAL	19.41	2
1	4	D	172	TIGHT THERMAL	12.16	2
1	1	A	109	MEDIUM THERMAL	13.63	5
1	2	B	109	MEDIUM THERMAL	9.98	5
1	3	C	109	MEDIUM THERMAL	18.81	5
1	4	D	109	MEDIUM THERMAL	12.78	5
2	1	A	194	MEDIUM POSITIONAL	0.22	0.75
2	2	B	194	MEDIUM POSITIONAL	0.17	0.75
2	3	C	194	MEDIUM POSITIONAL	0.17	0.75
2	4	D	194	MEDIUM POSITIONAL	0.23	0.75
2	1	A	1672	TIGHT THERMAL	6.52	2
2	2	B	1672	TIGHT THERMAL	7.09	2
2	3	C	1672	TIGHT THERMAL	6.07	2
2	4	D	1672	TIGHT THERMAL	7.13	2
2	1	A	194	MEDIUM THERMAL	7.76	5
2	2	B	194	MEDIUM THERMAL	8.62	5
2	3	C	194	MEDIUM THERMAL	9.66	5
2	4	D	194	MEDIUM THERMAL	8.76	5
3	1	A	28	MEDIUM POSITIONAL	0.8	0.75
3	2	B	28	MEDIUM POSITIONAL	0.61	0.75
3	3	C	28	MEDIUM POSITIONAL	0.46	0.75
3	4	D	28	MEDIUM POSITIONAL	0.82	0.75
3	1	A	11	LOOSE POSITIONAL	2.15	5
3	2	B	11	LOOSE POSITIONAL	1.38	5
3	3	C	11	LOOSE POSITIONAL	0.99	5
3	4	D	11	LOOSE POSITIONAL	1.28	5
3	1	A	28	MEDIUM THERMAL	21.17	5
3	2	B	28	MEDIUM THERMAL	15.99	5
3	3	C	28	MEDIUM THERMAL	11.16	5
3	4	D	28	MEDIUM THERMAL	17.7	5
3	1	A	11	LOOSE THERMAL	17.75	10
3	2	B	11	LOOSE THERMAL	17.65	10
3	3	C	11	LOOSE THERMAL	12.17	10
3	4	D	11	LOOSE THERMAL	18.67	10
4	1	A	24	MEDIUM POSITIONAL	0.2	0.75
4	2	B	24	MEDIUM POSITIONAL	0.26	0.75
4	3	C	24	MEDIUM POSITIONAL	0.3	0.75
4	4	D	24	MEDIUM POSITIONAL	0.19	0.75
4	1	A	22	LOOSE POSITIONAL	0.85	5
4	2	B	22	LOOSE POSITIONAL	0.88	5
4	3	C	22	LOOSE POSITIONAL	0.89	5
4	4	D	22	LOOSE POSITIONAL	0.85	5
4	1	A	24	MEDIUM THERMAL	11.02	5
4	2	B	24	MEDIUM THERMAL	9.38	5
4	3	C	24	MEDIUM THERMAL	15.05	5
4	4	D	24	MEDIUM THERMAL	15.58	5
4	1	A	22	LOOSE THERMAL	14.73	10
4	2	B	22	LOOSE THERMAL	13.36	10
4	3	C	22	LOOSE THERMAL	11.26	10
4	4	D	22	LOOSE THERMAL	16.64	10
5	1	A	78	MEDIUM POSITIONAL	0.11	0.75
5	2	B	78	MEDIUM POSITIONAL	0.13	0.75
5	3	C	78	MEDIUM POSITIONAL	0.1	0.75
5	4	D	78	MEDIUM POSITIONAL	0.26	0.75
5	1	A	88	TIGHT THERMAL	11.72	2
5	2	B	88	TIGHT THERMAL	7.1	2
5	3	C	88	TIGHT THERMAL	21.44	2
5	4	D	88	TIGHT THERMAL	16.53	2
5	1	A	78	MEDIUM THERMAL	14.18	5
5	2	B	78	MEDIUM THERMAL	12.5	5
5	3	C	78	MEDIUM THERMAL	19.07	5
5	4	D	78	MEDIUM THERMAL	15.56	5

LS refinement shell

Resolution: 3→3.077 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	95	-
R_work	0.286	1774	-
all	-	1869	-
obs	-	-	96.94 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.7441	0.1727	-0.0602	0.2098	-0.1594	0.3891	0.0359	-0.1384	-0.1082	0.0301	0.0687	-0.1045	0.0174	-0.3272	-0.1046	0.3146	-0.054	0.1174	0.4332	0.0624	0.2895	-11.979	7.324	41.724
2	3.4868	0.2872	3.932	0.9439	0.3702	4.5043	-0.0168	0.4251	0.5316	0.1237	-0.2688	-0.0343	0.1361	0.2998	0.2856	0.1144	-0.0653	0.1109	0.5571	0.4547	0.6347	37.819	22.191	12.079
3	7.4118	-0.7335	2.8287	0.4627	-0.1933	1.0994	-0.3369	-2.9432	1.139	-0.438	0.2595	-0.5446	-0.1259	-1.0705	0.0774	0.5166	-0.2253	0.4804	1.3096	-0.7072	0.6533	-5.007	18.149	54.039
4	3.1504	1.3749	3.5093	2.3733	1.8958	4.1837	0.1088	0.4311	0.0824	0.2625	-0.1006	0.1238	0.3605	0.5588	-0.0082	0.244	0.1221	0.0754	0.4553	0.0913	0.3369	43.891	7.501	20.619
5	0.3456	-0.2924	0.3873	0.8652	0.288	1.1594	0.0935	-0.0006	0.0007	0.231	0.0962	-0.0674	0.3182	-0.0196	-0.1897	0.5342	0.0705	-0.0667	0.1749	0.0965	0.2921	26.279	-6.549	42.075
6	0.4406	0.0269	-0.3365	1.724	0.0398	0.7213	-0.2467	-0.0677	0.1728	0.2805	0.0995	0.0052	-0.0212	0.0219	0.1472	0.4741	0.0683	-0.1715	0.2148	-0.0679	0.3164	24.382	28.031	50.631
7	0.3702	0.2954	-0.0472	1.2537	-0.2149	0.9009	-0.2413	0.2014	0.2481	0.1179	0.1673	0.0802	-0.0825	-0.0197	0.074	0.368	-0.0021	-0.16	0.2445	0.1292	0.4271	10.343	34.221	20.214
8	1.4023	0.0945	0.3155	1.6033	0.1175	0.4312	-0.0721	0.0528	-0.1251	-0.08	0.2016	0.1705	0.248	-0.0526	-0.1295	0.3887	-0.0825	-0.0165	0.2711	-0.0039	0.3326	3.956	-0.471	16.468

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 71
2	X-RAY DIFFRACTION	2	B	1 - 71
3	X-RAY DIFFRACTION	3	C	1 - 71
4	X-RAY DIFFRACTION	4	D	1 - 71
5	X-RAY DIFFRACTION	5	A	72 - 332
6	X-RAY DIFFRACTION	6	B	72 - 332
7	X-RAY DIFFRACTION	7	C	72 - 332
8	X-RAY DIFFRACTION	8	D	72 - 332

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Open data

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi