PDB-2ret: The crystal structure of a binary complex of two pseudopilins: Ep...

ID or keywords:

Entry

Database: PDB / ID: 2ret

Title

The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the Type 2 Secretion System of Vibrio vulnificus

Components

EpsJÉcole polyvalente Saint-Jérôme
Pseudopilin EpsI

Keywords

PROTEIN TRANSPORT / General Secretion Pathway /

Cholera / Pseudopilus / Type 4 Pilin Biogenesis /

Methylation

Function / homology

Function and homology information

protein secretion by the type II secretion system /

type II protein secretion system complex /

plasma membrane
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.21 Å

Authors

Yanez, M.E. / Korotkov, K.V. / Abendroth, J. / Hol, W.G.J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the type 2 secretion system of Vibrio vulnificus.
Authors: Yanez, M.E. / Korotkov, K.V. / Abendroth, J. / Hol, W.G.

History

Deposition	Sep 27, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / struct_ref_seq ...database_2 / struct_ref_seq / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 21, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2ret.cif.gz	220.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2ret.ent.gz	177.6 KB	Display	PDB format
PDBx/mmJSON format	2ret.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/re/2ret ftp://data.pdbj.org/pub/pdb/validation_reports/re/2ret	HTTPS FTP

-
Related structure data

Similar structure data	3hsi-1 6nte-d 1jgt-d 4tx3-d 6yqc-d 1xls-6 1mt5-3 6yq7-d Search similar-shape structures by Omokage search (details) 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	#211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: Pseudopilin EpsI

B: EpsJ

C: Pseudopilin EpsI

D: EpsJ

E: Pseudopilin EpsI

F: EpsJ

G: Pseudopilin EpsI

H: EpsJ

hetero molecules

130 kDa, 8 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)	63.288, 79.145, 82.079
Angle α, β, γ (deg.)	65.000, 69.190, 69.490
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	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	PRO	PRO	5	A	A	36 - 55	13 - 32
2	1	1	GLN	GLN	PRO	PRO	5	C	C	36 - 55	13 - 32
3	1	1	GLN	GLN	PRO	PRO	5	E	E	36 - 55	13 - 32
4	1	1	GLN	GLN	PRO	PRO	5	G	G	36 - 55	13 - 32
5	2	1	LYS	LYS	LEU	LEU	6	A	A	56 - 58	33 - 35
6	2	1	LYS	LYS	LEU	LEU	6	C	C	56 - 58	33 - 35
7	2	1	LYS	LYS	LEU	LEU	6	E	E	56 - 58	33 - 35
8	2	1	LYS	LYS	LEU	LEU	6	G	G	56 - 58	33 - 35
9	3	1	LYS	LYS	ALA	ALA	5	A	A	59 - 80	36 - 57
10	3	1	LYS	LYS	ALA	ALA	5	C	C	59 - 80	36 - 57
11	3	1	LYS	LYS	ALA	ALA	5	E	E	59 - 80	36 - 57
12	3	1	LYS	LYS	ALA	ALA	5	G	G	59 - 80	36 - 57
13	4	1	THR	THR	LEU	LEU	6	A	A	81 - 85	58 - 62
14	4	1	THR	THR	LEU	LEU	6	C	C	81 - 85	58 - 62
15	4	1	THR	THR	LEU	LEU	6	E	E	81 - 85	58 - 62
16	4	1	THR	THR	LEU	LEU	6	G	G	81 - 85	58 - 62
17	5	1	LEU	LEU	ALA	ALA	5	A	A	86 - 110	63 - 87
18	5	1	LEU	LEU	ALA	ALA	5	C	C	86 - 110	63 - 87
19	5	1	LEU	LEU	ALA	ALA	5	E	E	86 - 110	63 - 87
20	5	1	LEU	LEU	ALA	ALA	5	G	G	86 - 110	63 - 87
21	6	1	SER	SER	ASN	ASN	6	A	A	111 - 113	88 - 90
22	6	1	SER	SER	SER	SER	6	C	C	111	88
23	6	1	SER	SER	SER	SER	6	E	E	111	88
24	7	1	THR	THR	GLY	GLY	6	A	A	30 - 32	7 - 9
25	7	1	THR	THR	GLY	GLY	6	C	C	30 - 32	7 - 9
26	7	1	THR	THR	GLY	GLY	6	E	E	30 - 32	7 - 9
27	7	1	THR	THR	GLY	GLY	6	G	G	30 - 32	7 - 9
28	8	1	TYR	TYR	GLU	GLU	3	A	A	33 - 35	10 - 12
29	8	1	TYR	TYR	GLU	GLU	3	C	C	33 - 35	10 - 12
30	8	1	TYR	TYR	GLU	GLU	3	E	E	33 - 35	10 - 12
31	8	1	TYR	TYR	GLU	GLU	3	G	G	33 - 35	10 - 12
1	1	2	GLU	GLU	GLU	GLU	6	B	B	32 - 36	9 - 13
2	1	2	GLN	GLN	GLU	GLU	6	D	D	35 - 36	12 - 13
3	1	2	LEU	LEU	GLU	GLU	6	F	F	33 - 36	10 - 13
4	1	2	GLU	GLU	GLU	GLU	6	H	H	32 - 36	9 - 13
5	2	2	GLN	GLN	THR	THR	5	B	B	45 - 63	22 - 40
6	2	2	GLN	GLN	THR	THR	5	D	D	45 - 63	22 - 40
7	2	2	GLN	GLN	THR	THR	5	F	F	45 - 63	22 - 40
8	2	2	GLN	GLN	THR	THR	5	H	H	45 - 63	22 - 40
9	3	2	ARG	ARG	LYS	LYS	6	B	B	64 - 72	41 - 49
10	3	2	ARG	ARG	LYS	LYS	6	D	D	64 - 72	41 - 49
11	3	2	ARG	ARG	LYS	LYS	6	F	F	64 - 72	41 - 49
12	3	2	ARG	ARG	LYS	LYS	6	H	H	64 - 72	41 - 49
13	4	2	LYS	LYS	ALA	ALA	5	B	B	73 - 78	50 - 55
14	4	2	LYS	LYS	ALA	ALA	5	D	D	73 - 78	50 - 55
15	4	2	LYS	LYS	ALA	ALA	5	F	F	73 - 78	50 - 55
16	4	2	LYS	LYS	ALA	ALA	5	H	H	73 - 78	50 - 55
17	5	2	ASP	ASP	ASP	ASP	3	B	B	79 - 83	56 - 60
18	5	2	ASP	ASP	ASP	ASP	3	D	D	79 - 83	56 - 60
19	5	2	ASP	ASP	ASP	ASP	3	F	F	79 - 83	56 - 60
20	5	2	ASP	ASP	ASP	ASP	3	H	H	79 - 83	56 - 60
21	6	2	SER	SER	GLN	GLN	5	B	B	84 - 100	61 - 77
22	6	2	SER	SER	GLN	GLN	5	D	D	84 - 100	61 - 77
23	6	2	SER	SER	GLN	GLN	5	F	F	84 - 100	61 - 77
24	6	2	SER	SER	GLN	GLN	5	H	H	84 - 100	61 - 77
25	7	2	ASP	ASP	GLY	GLY	6	B	B	129 - 136	106 - 113
26	7	2	ASP	ASP	GLY	GLY	6	D	D	129 - 136	106 - 113
27	7	2	ASP	ASP	GLY	GLY	6	F	F	129 - 136	106 - 113
28	7	2	ASP	ASP	GLY	GLY	6	H	H	129 - 136	106 - 113
29	8	2	VAL	VAL	PRO	PRO	5	B	B	137 - 140	114 - 117
30	8	2	VAL	VAL	PRO	PRO	5	D	D	137 - 140	114 - 117
31	8	2	VAL	VAL	PRO	PRO	5	F	F	137 - 140	114 - 117
32	8	2	VAL	VAL	PRO	PRO	5	H	H	137 - 140	114 - 117
33	9	2	LYS	LYS	TRP	TRP	6	B	B	156 - 158	133 - 135
34	9	2	LYS	LYS	TRP	TRP	6	D	D	156 - 158	133 - 135
35	9	2	LYS	LYS	TRP	TRP	6	F	F	156 - 158	133 - 135
36	9	2	LYS	LYS	TRP	TRP	6	H	H	156 - 158	133 - 135
37	10	2	ILE	ILE	ASN	ASN	5	B	B	159 - 194	136 - 171
38	10	2	ILE	ILE	ASN	ASN	5	D	D	159 - 194	136 - 171
39	10	2	ILE	ILE	ASN	ASN	5	F	F	159 - 194	136 - 171
40	10	2	ILE	ILE	ASN	ASN	5	H	H	159 - 194	136 - 171
41	11	2	LEU	LEU	HOH	HOH	6	B	B - N	195 - 199	172
42	11	2	LEU	LEU	HOH	HOH	6	D	D - P	195 - 199	172
43	11	2	LEU	LEU	HOH	HOH	6	F	F - R	195 - 199	172
44	11	2	LEU	LEU	HOH	HOH	6	H	H - T	195 - 199	172
45	12	2	ASN	ASN	LEU	LEU	3	B	B	42 - 44	19 - 21
46	12	2	ASN	ASN	LEU	LEU	3	D	D	42 - 44	19 - 21
47	12	2	ASN	ASN	LEU	LEU	3	F	F	42 - 44	19 - 21
48	12	2	ASN	ASN	LEU	LEU	3	H	H	42 - 44	19 - 21
49	13	2	GLN	GLN	LYS	LYS	3	B	B	101 - 110	78 - 87
50	13	2	GLN	GLN	LYS	LYS	3	D	D	101 - 110	78 - 87
51	13	2	GLN	GLN	LYS	LYS	3	F	F	101 - 110	78 - 87
52	13	2	GLN	GLN	LYS	LYS	3	H	H	101 - 110	78 - 87
53	14	2	VAL	VAL	PRO	PRO	5	B	B	111 - 128	88 - 105
54	14	2	VAL	VAL	PRO	PRO	5	D	D	111 - 128	88 - 105
55	14	2	VAL	VAL	PRO	PRO	5	F	F	111 - 128	88 - 105
56	14	2	VAL	VAL	PRO	PRO	5	H	H	111 - 128	88 - 105
57	15	2	LEU	LEU	VAL	VAL	3	B	B	141 - 145	118 - 122
58	15	2	LEU	LEU	VAL	VAL	3	D	D	141 - 145	118 - 122
59	15	2	LEU	LEU	VAL	VAL	3	F	F	141 - 145	118 - 122
60	15	2	LEU	LEU	VAL	VAL	3	H	H	141 - 145	118 - 122
61	16	2	GLU	GLU	GLY	GLY	5	B	B	146 - 155	123 - 132
62	16	2	GLU	GLU	GLY	GLY	5	D	D	146 - 155	123 - 132
63	16	2	GLU	GLU	GLY	GLY	5	F	F	146 - 155	123 - 132
64	16	2	GLU	GLU	GLY	GLY	5	H	H	146 - 155	123 - 132

NCS ensembles :

ID
1
2

#1: Protein	Pseudopilin EpsI Mass: 11689.310 Da / Num. of mol.: 4 / Fragment: Residues 58-143 / Mutation: E128T, K129T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: epsi / Plasmid: pCDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MPZ1
#2: Protein	EpsJ / École polyvalente Saint-Jérôme Mass: 20734.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: epsj / Plasmid: pCDF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MPZ0*PLUS
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.86 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 10-15% PEG 4000 and 0.1 M MnCl2, protein buffer: 20 mM Tris-Hcl (pH 7.8), 250 mM NaCl, 1 mM EDTA, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97903 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 29, 2007
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror

Radiation

Monochromator: Double crystal monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97903 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 63933 / % possible obs: 97.5 % / Redundancy: 3.8 % / R_merge(I) obs: 0.085 / Χ²: 1.041 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.2-2.28	2.7	0.501	6027	1.081	1	91.8
2.28-2.37	3.3	0.421	6303	1.075	1	96.5
2.37-2.48	3.8	0.33	6460	1.069	1	97.7
2.48-2.61	3.9	0.258	6384	1.056	1	97.8
2.61-2.77	4	0.184	6430	1.041	1	98
2.77-2.99	4	0.133	6479	1.046	1	98.4
2.99-3.29	4	0.088	6444	1.022	1	98.4
3.29-3.76	4	0.062	6460	1.015	1	98.6
3.76-4.74	3.9	0.053	6466	1.028	1	98.7
4.74-50	3.9	0.063	6480	1.003	1	98.6

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.1	phasing
REFMAC	5.3.0037	refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.21→40.39 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.918 / SU B: 11.567 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.245	3205	5.1 %	RANDOM
R_work	0.185	-	-	-
obs	0.188	63270	96.26 %	-

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: 16.943 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.34 Å²	0.5 Å²	-0.28 Å²
2-	-	0.02 Å²	-0.16 Å²
3-	-	-	-0.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.21→40.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7597	0	4	611	8212

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	7839
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5327
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.951	10652
X-RAY DIFFRACTION	r_angle_other_deg	0.922	3	12928
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.759	5	956
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.982	23.591	362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.611	15	1346
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.582	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1191
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	8618
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1608
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	1353
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	5439
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	3602
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	4542
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	463
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.087	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.251	0.2	3
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.357	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.245	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.23	0.2	29
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.254	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.671	1.5	4788
X-RAY DIFFRACTION	r_mcbond_other	0.161	1.5	1912
X-RAY DIFFRACTION	r_mcangle_it	1.273	2	7701
X-RAY DIFFRACTION	r_scbond_it	2.537	3	3229
X-RAY DIFFRACTION	r_scangle_it	3.693	4.5	2943

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	18	TIGHT POSITIONAL	0.06	0.05
1	1	C	18	TIGHT POSITIONAL	0.03	0
1	1	E	18	TIGHT POSITIONAL	0.09	0
1	1	G	18	TIGHT POSITIONAL	0.07	0
1	1	A	399	MEDIUM POSITIONAL	0.13	0.5
1	1	C	399	MEDIUM POSITIONAL	0.14	0
1	1	E	399	MEDIUM POSITIONAL	0.15	0
1	1	G	399	MEDIUM POSITIONAL	0.1	0
1	1	A	574	LOOSE POSITIONAL	0.3	5
1	1	C	574	LOOSE POSITIONAL	0.32	0.01
1	1	E	574	LOOSE POSITIONAL	0.31	0
1	1	G	574	LOOSE POSITIONAL	0.27	0
1	1	A	18	TIGHT THERMAL	0.35	0.5
1	1	C	18	TIGHT THERMAL	0.38	0.03
1	1	E	18	TIGHT THERMAL	0.22	0
1	1	G	18	TIGHT THERMAL	0.62	0
1	1	A	399	MEDIUM THERMAL	0.75	2
1	1	C	399	MEDIUM THERMAL	0.76	0.01
1	1	E	399	MEDIUM THERMAL	0.59	0
1	1	G	399	MEDIUM THERMAL	0.47	0
1	1	A	574	LOOSE THERMAL	0.67	10
1	1	C	574	LOOSE THERMAL	0.68	0.02
1	1	E	574	LOOSE THERMAL	0.63	0
1	1	G	574	LOOSE THERMAL	0.55	0
2	2	B	134	TIGHT POSITIONAL	0.17	0.05
2	2	D	134	TIGHT POSITIONAL	0.14	0
2	2	F	134	TIGHT POSITIONAL	0.14	0
2	2	H	134	TIGHT POSITIONAL	0.16	0
2	2	B	641	MEDIUM POSITIONAL	0.29	0.5
2	2	D	641	MEDIUM POSITIONAL	0.12	0
2	2	F	641	MEDIUM POSITIONAL	0.19	0
2	2	H	641	MEDIUM POSITIONAL	0.21	0
2	2	B	1281	LOOSE POSITIONAL	0.63	5
2	2	D	1281	LOOSE POSITIONAL	0.5	0
2	2	F	1281	LOOSE POSITIONAL	0.69	0
2	2	H	1281	LOOSE POSITIONAL	0.6	0
2	2	B	134	TIGHT THERMAL	2.7	0.5
2	2	D	134	TIGHT THERMAL	2.09	0
2	2	F	134	TIGHT THERMAL	2.31	0
2	2	H	134	TIGHT THERMAL	3.18	0
2	2	B	641	MEDIUM THERMAL	3.81	2
2	2	D	641	MEDIUM THERMAL	1.83	0
2	2	F	641	MEDIUM THERMAL	1.87	0
2	2	H	641	MEDIUM THERMAL	3.3	0
2	2	B	1281	LOOSE THERMAL	3.62	10
2	2	D	1281	LOOSE THERMAL	2.21	0.01
2	2	F	1281	LOOSE THERMAL	2.35	0
2	2	H	1281	LOOSE THERMAL	3.11	0

LS refinement shell

Resolution: 2.209→2.266 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	168	-
R_work	0.242	3506	-
all	-	3674	-
obs	-	-	75.4 %

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	3.0968	-1.0281	-0.4974	9.8485	6.739	14.4419	-0.1614	-0.0692	-0.129	0.2144	-0.0519	0.2837	0.2281	0.1349	0.2133	0.0231	-0.0403	-0.0031	0.1393	0.0553	0.117	95.22	98.983	32.829
2	8.3394	-3.7668	-2.3991	10.3015	0.3698	7.4869	-0.0913	0.8289	-0.8266	-1.1397	-0.0089	-0.109	-0.0472	0.405	0.1003	0.0793	-0.0343	-0.0363	0.364	-0.0294	0.1283	105.396	95.02	27.954
3	3.4546	-1.302	0.6051	5.8324	1.9934	4.5647	0.0382	0.0714	-0.4054	0.66	-0.2487	0.1733	0.7361	0.0974	0.2106	0.0783	-0.0624	0.0216	0.0796	-0.0215	0.055	101.158	93.359	32.984
4	5.284	2.5324	1.7094	7.908	2.383	4.5167	-0.0877	0.2809	-0.6435	-0.2005	0.0633	-0.1198	0.1703	0.1226	0.0244	0.0275	-0.0079	0.0501	0.0436	-0.0047	0.1116	97.519	88.311	31.669
5	3.2284	-0.0591	0.1726	2.9915	1.4143	6.1055	0.0565	-0.1308	0.1558	-0.136	0.1594	0.1198	-0.3183	-0.0369	-0.2159	0.0677	-0.0445	0.0174	0.1383	0.0179	0.2025	83.581	108.278	25.885
6	3.666	-0.0479	0.4386	1.5261	0.3249	2.3874	0.0048	0.0257	0.0425	-0.0301	-0.0466	0.0751	-0.0218	-0.2101	0.0417	0.0578	-0.0217	0.0245	0.0924	0.0296	0.0436	79.106	109.755	17.835
7	12.1833	0.0176	24.9662	17.6716	4.9503	63.1435	-0.305	-0.173	1.0268	-2.4096	-1.4009	0.9768	-4.7646	-2.019	1.706	0.2373	0.0894	-0.1295	0.3858	0.0232	0.156	72.576	114.656	11.629
8	3.8005	-0.6631	0.2189	3.7201	0.6544	3.1298	0.0269	0.4071	0.0577	-0.3243	0.082	-0.2492	-0.107	0.2629	-0.1089	0.0994	-0.0582	0.0007	0.1148	0.0594	0.124	92.11	108.259	19.515
9	2.6691	-0.5113	0.5165	15.0634	1.5972	5.3706	-0.1833	0.1027	-0.0565	-0.3725	0.3421	-0.2277	-0.1798	0.1634	-0.1589	0.0099	0.003	0.0063	0.1334	0.012	0.1729	57.595	106.701	18.665
10	18.5841	-3.0529	-2.9461	11.3227	4.7731	8.1222	-0.2495	0.6347	-1.6961	0.0278	-0.6688	1.1165	0.614	-0.8099	0.9182	0.0501	0.0098	0.0008	0.0837	0.0391	0.4911	47.791	101.443	16.133
11	5.374	-1.2285	0.9463	6.9955	0.35	0.5277	0.1138	0.6213	-0.0199	-1.1676	-0.1784	0.2365	-0.3621	-0.2026	0.0645	0.0846	0.0488	-0.0013	0.0757	0.0098	0.133	52.28	104.658	12.812
12	8.0301	-4.9858	-2.9724	9.7107	4.1392	5.0451	0.2041	0.8836	-0.1715	-0.7341	-0.2013	0.0924	-0.0173	-0.1723	-0.0029	0.0473	0.0141	-0.0172	0.035	-0.0435	0.0342	55.951	103.207	8.841
13	3.0059	0.7201	0.1964	4.2901	0.0899	2.8247	-0.082	-0.1318	0.0445	0.0585	0.0317	0.032	0.1548	0.2346	0.0504	0.0551	0.0055	0.0191	0.173	0.0179	0.1403	68.299	102.869	30.542
14	5.656	-0.5921	-0.9707	3.2907	0.8428	1.8794	0.1846	-0.0595	-0.0757	-0.0517	-0.0794	-0.2835	-0.0506	0.0595	-0.1052	0.0879	-0.0113	-0.0134	0.0534	0.0729	0.1281	74.087	94.447	33.066
15	8.3115	-1.9976	0.1889	4.4835	0.5801	3.0141	-0.1592	-0.9309	-0.0214	0.6247	0.1095	-0.2016	0.0427	0.1187	0.0498	0.1181	-0.0198	-0.0235	0.1632	0.0333	0.0697	71.651	103.737	39.364
16	4.393	0.0947	0.0358	3.6287	1.1415	4.21	0.0245	-0.1956	-0.59	0.2927	-0.0697	0.1123	0.5285	-0.1187	0.0451	0.0337	-0.0139	0.0281	0.0691	0.0501	0.1072	58.889	94.746	30.371
17	5.9034	-3.7765	-0.965	11.5664	4.5748	7.202	0.0758	-0.1397	-0.06	-0.2803	0.1279	-0.0432	-0.2324	0.389	-0.2037	0.1019	-0.0413	0.0154	0.0817	0.0517	0.143	80.934	57.48	17.829
18	5.6561	0.8402	-0.1415	9.6481	-0.0584	8.8363	0.0644	-0.5123	0.3985	1.3093	-0.3238	0.8224	-0.2843	-0.4846	0.2593	0.2576	0.0363	0.0932	0.1022	0.0819	0.2189	76.109	57.27	28.785
19	1.6943	-0.3672	-0.7047	9.1318	1.138	5.5347	0.0905	-0.4548	-0.0504	0.8912	0.3111	-0.9012	-0.1436	0.2154	-0.4017	0.0777	0.023	-0.0022	-0.0285	0.0012	0.1332	82.256	57.596	25.905
20	1.9032	1.217	0.121	9.9825	0.4164	2.6644	-0.0037	-0.2544	0.1139	0.9276	0.1647	-0.5153	-0.2398	0.3052	-0.161	0.0955	-0.0355	-0.0017	0.0316	-0.048	0.1184	85.376	62.292	26.143
21	4.1241	-2.1057	-0.9469	5.8748	0.5869	3.341	-0.0524	0.1603	-0.1003	-0.3243	-0.135	0.2395	0.1411	-0.0091	0.1874	0.201	-0.0038	0.0009	0.1521	0.0657	0.1312	73.725	62.099	4.233
22	1.2695	-1.6104	-0.5133	3.0693	-1.3118	3.9611	0.1066	0.0568	-0.1048	-0.2032	-0.0371	0.0847	0.255	-0.1533	-0.0695	0.0797	0.03	-0.0153	0.1211	0.0047	0.0919	67.979	67.732	0.121
23	2.2815	-0.8423	0.6438	7.1085	-1.8954	3.9477	0.0894	0.3683	0.0239	-0.8533	-0.053	1.0036	0.1298	-0.3682	-0.0363	0.317	0.0738	-0.134	0.2524	-0.0055	0.222	68.522	63.095	-4.062
24	3.5005	-1.3819	-0.3876	7.2068	1.3473	4.9216	0.0121	-0.14	-0.0216	0.2777	-0.1928	0.9257	-0.1749	-0.7134	0.1807	0.0372	-0.0077	0.042	0.096	0.0232	0.126	65.684	62.096	14.041
25	6.6631	4.1583	3.6231	12.58	7.1256	8.9432	-0.0424	-0.0948	0.1063	0.3169	-0.0779	0.4502	0.0681	0.0845	0.1203	0.1774	-0.0179	0.0168	0.1662	0.0468	0.041	76.485	81.223	-15.034
26	8.6342	-0.4513	-5.7493	13.4606	5.6845	13.6544	0.3584	-0.5277	0.9123	-0.2265	0.4348	-0.6256	-1.7724	0.9609	-0.7933	0.4142	-0.1615	-0.0441	0.2127	0.0188	0.0533	80.08	92.11	-18.516
27	2.1405	1.3419	0.8839	6.961	2.1732	8.0794	0.0295	-0.0427	0.4324	-0.0094	-0.2972	0.6645	-0.4711	-0.4867	0.2676	0.1804	-0.0273	-0.0173	0.1451	-0.0367	0.0211	74.279	88.706	-17.486
28	2.78	-0.3587	-0.3702	3.4747	2.3121	11.7273	-0.0232	-0.1119	0.2665	0.0258	-0.0829	0.2611	-0.8916	-0.5069	0.1061	0.1844	0.008	0.0329	0.0465	-0.0345	0.0303	70.718	89.688	-13.653
29	1.8535	-0.0497	0.1761	3.4336	0.1672	5.649	0.0289	0.0037	0.0095	-0.0781	0.2003	-0.0328	0.5892	0.3498	-0.2292	0.106	0.0301	-0.0001	0.1262	0.0345	0.0263	84.078	70.063	-6.729
30	0.9369	0.9088	1.0113	3.5058	-1.5169	4.6171	0.1831	0.0436	-0.1109	-0.0893	-0.192	-0.2487	0.1636	0.4074	0.0089	0.0637	0.0234	-0.0527	0.1919	0.0084	0.1113	90.03	68.977	0.822
31	3.8277	-1.5711	3.6153	7.4289	4.7742	17.3784	-0.2674	-0.2973	-0.3006	0.9639	0.6393	-0.9551	0.9651	1.8606	-0.3718	0.3194	0.1092	-0.1263	0.4494	0.0577	0.2227	90.957	63.066	4.322
32	3.9665	-0.638	0.9406	4.952	2.287	7.67	-0.0678	0.0733	0.3668	-0.1311	0.2975	-0.7474	-0.6359	1.0297	-0.2296	0.0426	-0.0644	0.0124	0.2118	0.0121	0.0736	91.371	79.268	-9.444

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	30 - 56	7 - 33
2	X-RAY DIFFRACTION	2	A	A	57 - 66	34 - 43
3	X-RAY DIFFRACTION	3	A	A	67 - 83	44 - 60
4	X-RAY DIFFRACTION	4	A	A	84 - 113	61 - 90
5	X-RAY DIFFRACTION	5	B	B	32 - 73	9 - 50
6	X-RAY DIFFRACTION	6	B	B	74 - 127	51 - 104
7	X-RAY DIFFRACTION	7	B	B	128 - 135	105 - 112
8	X-RAY DIFFRACTION	8	B	B	136 - 197	113 - 174
9	X-RAY DIFFRACTION	9	C	C	30 - 56	7 - 33
10	X-RAY DIFFRACTION	10	C	C	58 - 66	35 - 43
11	X-RAY DIFFRACTION	11	C	C	67 - 83	44 - 60
12	X-RAY DIFFRACTION	12	C	C	84 - 111	61 - 88
13	X-RAY DIFFRACTION	13	D	D	35 - 75	12 - 52
14	X-RAY DIFFRACTION	14	D	D	76 - 112	53 - 89
15	X-RAY DIFFRACTION	15	D	D	113 - 147	90 - 124
16	X-RAY DIFFRACTION	16	D	D	148 - 197	125 - 174
17	X-RAY DIFFRACTION	17	E	E	30 - 56	7 - 33
18	X-RAY DIFFRACTION	18	E	E	57 - 66	34 - 43
19	X-RAY DIFFRACTION	19	E	E	67 - 83	44 - 60
20	X-RAY DIFFRACTION	20	E	E	84 - 111	61 - 88
21	X-RAY DIFFRACTION	21	F	F	33 - 75	10 - 52
22	X-RAY DIFFRACTION	22	F	F	76 - 125	53 - 102
23	X-RAY DIFFRACTION	23	F	F	126 - 147	103 - 124
24	X-RAY DIFFRACTION	24	F	F	148 - 196	125 - 173
25	X-RAY DIFFRACTION	25	G	G	30 - 56	7 - 33
26	X-RAY DIFFRACTION	26	G	G	57 - 66	34 - 43
27	X-RAY DIFFRACTION	27	G	G	67 - 83	44 - 60
28	X-RAY DIFFRACTION	28	G	G	84 - 110	61 - 87
29	X-RAY DIFFRACTION	29	H	H	32 - 75	9 - 52
30	X-RAY DIFFRACTION	30	H	H	76 - 125	53 - 102
31	X-RAY DIFFRACTION	31	H	H	126 - 141	103 - 118
32	X-RAY DIFFRACTION	32	H	H	142 - 196	119 - 173

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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