PDB-3by7: CRYSTAL STRUCTURE OF A PROTEIN STRUCTURALLY SIMILAR TO SM/LSM-LIK...

ID or keywords:

Entry

Database: PDB / ID: 3by7

Title

CRYSTAL STRUCTURE OF A PROTEIN STRUCTURALLY SIMILAR TO SM/LSM-LIKE RNA-BINDING PROTEINS (JCVI_PEP_1096686650277) FROM UNCULTURED MARINE ORGANISM AT 2.60 A RESOLUTION

Components

uncharacterized protein

Keywords

UNKNOWN FUNCTION /

METAGENOMICS /

STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG /

PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

SH3 type barrels. - #100 / SH3 type barrels. / Roll / Mainly Beta

Function and homology information

Biological species

uncultured marine organism (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.6 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: Proteins / Year: 2009
Title: Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.
Authors: Das, D. / Kozbial, P. / Axelrod, H.L. / Miller, M.D. / McMullan, D. / Krishna, S.S. / Abdubek, P. / Acosta, C. / Astakhova, T. / Burra, P. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. ...

History

Deposition	Jan 15, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Feb 1, 2023	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3by7.cif.gz	86.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3by7.ent.gz	68.5 KB	Display	PDB format
PDBx/mmJSON format	3by7.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/by/3by7 ftp://data.pdbj.org/pub/pdb/validation_reports/by/3by7	HTTPS FTP

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Related structure data

Similar structure data	6ial-1 3chb-d 6hmy-2 1ct1-d 2chb-d 5lzi-d 3q1g-1 1md2-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 380229

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein

B: uncharacterized protein

C: uncharacterized protein

D: uncharacterized protein

E: uncharacterized protein

55.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, light scattering

Unit cell

Length a, b, c (Å)	108.250, 77.180, 71.470
Angle α, β, γ (deg.)	90.000, 113.820, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	ASN	5	A	A	2 - 3	3 - 4
2	1	LYS	ASN	5	B	B	2 - 3	3 - 4
3	1	LYS	ASN	5	C	C	2 - 3	3 - 4
4	1	LYS	ASN	5	D	D	2 - 3	3 - 4
5	1	ASN	ASN	5	E	E	3	4
6	2	ILE	MSE	2	A	A	4 - 7	5 - 8
7	2	ILE	MSE	2	B	B	4 - 7	5 - 8
8	2	ILE	MSE	2	C	C	4 - 7	5 - 8
9	2	ILE	MSE	2	D	D	4 - 7	5 - 8
10	2	ILE	MSE	2	E	E	4 - 7	5 - 8
11	3	ARG	ARG	3	A	A	8	9
12	3	ARG	ARG	3	B	B	8	9
13	3	ARG	ARG	3	C	C	8	9
14	3	ARG	ARG	3	D	D	8	9
15	3	ARG	ARG	3	E	E	8	9
16	4	LEU	GLN	2	A	A	9 - 38	10 - 39
17	4	LEU	GLN	2	B	B	9 - 38	10 - 39
18	4	LEU	ALA	2	C	C	9 - 39	10 - 40
19	4	LEU	GLN	2	D	D	9 - 38	10 - 39
20	4	LEU	MSE	2	E	E	9 - 37	10 - 38
21	5	VAL	GLN	5	A	A	45 - 46	46 - 47
22	5	VAL	GLN	5	B	B	45 - 46	46 - 47
23	5	VAL	GLN	5	C	C	45 - 46	46 - 47
24	5	VAL	GLN	5	D	D	45 - 46	46 - 47
25	5	VAL	GLN	5	E	E	45 - 46	46 - 47
26	6	LEU	ILE	2	A	A	47 - 69	48 - 70
27	6	LEU	ILE	2	B	B	47 - 69	48 - 70
28	6	LEU	ILE	2	C	C	47 - 69	48 - 70
29	6	LEU	ILE	2	D	D	47 - 69	48 - 70
30	6	LEU	ILE	2	E	E	47 - 69	48 - 70
31	7	THR	THR	5	A	A	70	71
32	7	THR	THR	5	B	B	70	71
33	7	THR	THR	5	C	C	70	71
34	7	THR	THR	5	D	D	70	71
35	7	THR	THR	5	E	E	70	71
36	8	ILE	ASP	2	A	A	71 - 76	72 - 77
37	8	ILE	ASP	2	B	B	71 - 76	72 - 77
38	8	ILE	ASP	2	C	C	71 - 76	72 - 77
39	8	ILE	ASP	2	D	D	71 - 76	72 - 77
40	8	ILE	ASP	2	E	E	71 - 76	72 - 77
41	9	ASP	ASP	5	A	A	77	78
42	9	ASP	ASP	5	B	B	77	78
43	9	ASP	ASP	5	C	C	77	78
44	9	ASP	ASP	5	D	D	77	78
45	9	ASP	ASP	5	E	E	77	78
46	10	ILE	LYS	2	A	A	78 - 80	79 - 81
47	10	ILE	LYS	2	B	B	78 - 80	79 - 81
48	10	ILE	LYS	2	C	C	78 - 80	79 - 81
49	10	ILE	LYS	2	D	D	78 - 80	79 - 81
50	10	ILE	LYS	2	E	E	78 - 80	79 - 81
51	11	SER	SER	3	A	A	81	82
52	11	SER	SER	3	B	B	81	82
53	11	SER	SER	3	C	C	81	82
54	11	SER	SER	3	D	D	81	82
55	11	SER	SER	3	E	E	81	82
56	12	TYR	SER	2	A	A	82 - 84	83 - 85
57	12	TYR	SER	2	B	B	82 - 84	83 - 85
58	12	TYR	SER	2	C	C	82 - 84	83 - 85
59	12	TYR	SER	2	D	D	82 - 84	83 - 85
60	12	TYR	SER	2	E	E	82 - 84	83 - 85
61	13	HIS	THR	5	A	A	85 - 86	86 - 87
62	13	HIS	THR	5	B	B	85 - 86	86 - 87
63	13	HIS	THR	5	C	C	85 - 86	86 - 87
64	13	HIS	THR	5	D	D	85 - 86	86 - 87
65	13	HIS	HIS	5	E	E	85	86

Details

THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 CHAINS FORMING A PENTAMER AS JUDGED BY CRYSTAL PACKING ANALYSIS. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A PENTAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

#1: Protein	uncharacterized protein Mass: 11147.415 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured marine organism (environmental samples) Gene: Synthetic gene: The gene product was based on JCVI_PEP_1096686650277 from the Sorcerer II Global Ocean Sampling experiment Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE (UNIPROTKB) DATABASE AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT THE J. CRAIG VENTER INSTITUTE WITH ACCESSION CODE JCVI_PEP_1096686650277, FROM THE UNIPROT ARCHIVE (UNIPARC) UNDER ACCESSION ID UPI000148A153 AND FROM THE UNIPROT METAGENOMIC AND ENVIRONMENTAL SEQUENCES (UNIMES) DATABASE UNDER ACCESSION ID MES00005880000.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: NANODROP, 0.2M Ca Acetate, 20.0% PEG 3350, No Buffer pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.95373, 0.97957, 0.97942

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.95373	1
2	0.97957	1
3	0.97942	1

Reflection

Resolution: 2.6→27.057 Å / Num. obs: 16122 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 58.562 Å² / R_merge(I) obs: 0.047 / Net I/σ(I): 9.46

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
2.6-2.69	0.404	1.8	1918	2946	1	92.4
2.69-2.8	0.367	2.1	2072	3203	1	96.2
2.8-2.93	0.32	2.5	2109	3225	1	96.5
2.93-3.08	0.191	4	1986	3068	1	96.5
3.08-3.27	0.154	5.4	2009	3111	1	96.6
3.27-3.52	0.076	8.4	2045	3151	1	97
3.52-3.88	0.057	11.4	2069	3257	1	96.8
3.88-4.43	0.035	15.6	1972	3104	1	96.6
4.43-5.57	0.028	20.8	2030	3164	1	96.5
5.57-27.057	0.021	22.6	1982	3047	1	91.6

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
XDS		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.6→27.057 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.897 / SU B: 36.405 / SU ML: 0.331 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.616 / ESU R Free: 0.339
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.285	825	5.1 %	RANDOM
R_work	0.235	-	-	-
obs	0.238	16120	96.58 %	-

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 mean: 32.898 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.18 Å²	0 Å²	-0.3 Å²
2-	-	4.18 Å²	0 Å²
3-	-	-	-4.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→27.057 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3024	0	0	7	3031

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3068
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	1944
X-RAY DIFFRACTION	r_angle_refined_deg	1.247	1.973	4184
X-RAY DIFFRACTION	r_angle_other_deg	0.871	3	4873
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.42	5	395
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.758	26.667	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.684	15	529
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.625	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	543
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3256
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	486
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	551
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	1927
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1507
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	1687
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	61
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.125	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.233	0.2	15
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.242	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.785	2.5	2174
X-RAY DIFFRACTION	r_mcbond_other	0.268	2.5	797
X-RAY DIFFRACTION	r_mcangle_it	1.027	4	3327
X-RAY DIFFRACTION	r_scbond_it	2.381	6	1131
X-RAY DIFFRACTION	r_scangle_it	3.747	8	857

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	413	TIGHT POSITIONAL	0.03	0.05
2	B	413	TIGHT POSITIONAL	0.04	0.05
3	C	413	TIGHT POSITIONAL	0.03	0.05
4	D	413	TIGHT POSITIONAL	0.03	0.05
5	E	413	TIGHT POSITIONAL	0.03	0.05
1	A	424	MEDIUM POSITIONAL	0.23	0.5
2	B	424	MEDIUM POSITIONAL	0.37	0.5
3	C	424	MEDIUM POSITIONAL	0.24	0.5
4	D	424	MEDIUM POSITIONAL	0.28	0.5
5	E	424	MEDIUM POSITIONAL	0.23	0.5
1	A	40	LOOSE POSITIONAL	0.59	5
2	B	40	LOOSE POSITIONAL	1.17	5
3	C	40	LOOSE POSITIONAL	0.73	5
4	D	40	LOOSE POSITIONAL	0.67	5
5	E	40	LOOSE POSITIONAL	0.87	5
1	A	413	TIGHT THERMAL	0.06	0.5
2	B	413	TIGHT THERMAL	0.06	0.5
3	C	413	TIGHT THERMAL	0.06	0.5
4	D	413	TIGHT THERMAL	0.06	0.5
5	E	413	TIGHT THERMAL	0.04	0.5
1	A	424	MEDIUM THERMAL	0.55	2
2	B	424	MEDIUM THERMAL	0.59	2
3	C	424	MEDIUM THERMAL	0.53	2
4	D	424	MEDIUM THERMAL	0.46	2
5	E	424	MEDIUM THERMAL	0.37	2
1	A	40	LOOSE THERMAL	1.12	10
2	B	40	LOOSE THERMAL	2.35	10
3	C	40	LOOSE THERMAL	1.17	10
4	D	40	LOOSE THERMAL	2.15	10
5	E	40	LOOSE THERMAL	2.17	10

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	59	-
R_work	0.365	1120	-
all	-	1179	-
obs	-	-	94.09 %

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	8.5346	-0.3198	-3.0385	5.9261	2.1947	6.9862	0.1445	0.3224	0.6042	0.1944	-0.0262	0.3556	-0.7899	-1.0617	-0.1183	0.0716	0.1415	-0.0416	0.0748	0.0775	0.1339	-69.0444	41.4362	11.2369
2	2.8904	0.105	0.0704	4.4254	1.0722	9.8149	0.2829	-0.6578	0.3067	0.1306	-0.2738	-0.2933	-0.4839	1.0906	-0.009	0.0363	-0.2539	-0.0278	0.32	-0.0793	0.0915	-48.1945	38.668	20.0615
3	7.2333	0.5126	-1.3973	5.4258	-1.1681	4.8179	-0.2595	0.2741	-0.0959	-0.1367	0.0412	0.4207	0.4408	-1.443	0.2184	0.2037	-0.3944	-0.0246	0.454	-0.1728	0.1216	-78.0402	21.2478	7.4305
4	5.8483	0.3562	2.2491	4.2232	-0.3556	4.7359	-0.2747	-0.5854	-0.4591	0.3804	0.2204	-0.0792	0.6318	1.0178	0.0543	0.3088	0.5132	0.0345	0.4399	0.251	0.1147	-43.8915	16.475	22.524
5	5.2511	-0.6147	1.658	4.3283	-1.4497	2.5506	-0.3119	-0.5812	-0.9067	0.0162	-0.2326	0.3142	1.4759	0.1624	0.5445	0.7895	-0.1163	0.207	0.1775	0.0061	0.3439	-62.6117	5.8266	13.6023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 86	3 - 87
2	X-RAY DIFFRACTION	2	B	B	2 - 87	3 - 88
3	X-RAY DIFFRACTION	3	C	C	2 - 87	3 - 88
4	X-RAY DIFFRACTION	4	D	D	2 - 90	3 - 91
5	X-RAY DIFFRACTION	5	E	E	3 - 85	4 - 86

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