PDB-2jes: Portal protein (gp6) from bacteriophage SPP1

ID or keywords:

Entry

Database: PDB / ID: 2jes

Title

Portal protein (gp6) from bacteriophage SPP1

Components

PORTAL PROTEIN
UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

Keywords

VIRAL PROTEIN / BACTERIOPHAGE SPP1 / DNA TRANSLOCATION /

MOLECULAR MOTOR / VIRAL PORTAL PROTEIN

Function / homology

Portal protein, SPP1-type / Portal protein / Phage portal protein, SPP1 Gp6-like / viral DNA genome packaging, headful / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral procapsid / : / Portal protein

Function and homology information

Biological species

BACTERIOPHAGE SPP1 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 3.4 Å

Authors

Lebedev, A.A. / Krause, M.H. / Isidro, A.L. / Vagin, A.A. / Orlova, E.V. / Turner, J. / Dodson, E.J. / Tavares, P. / Antson, A.A.

Citation

Journal: Embo J. / Year: 2007
Title: Structural Framework for DNA Translocation Via the Viral Portal Protein
Authors: Lebedev, A.A. / Krause, M.H. / Isidro, A.L. / Vagin, A.A. / Orlova, E.V. / Turner, J. / Dodson, E.J. / Tavares, P. / Antson, A.A.

History

Deposition	Jan 21, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 29, 2017	Group: Derived calculations / Structure summary

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2jes.cif.gz	850.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2jes.ent.gz	696.8 KB	Display	PDB format
PDBx/mmJSON format	2jes.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	6qx5-d 30138 6tjp-d 7cg3-d 3ja7-d 3323 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	#147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: PORTAL PROTEIN

B: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

C: PORTAL PROTEIN

D: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

E: PORTAL PROTEIN

F: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

G: PORTAL PROTEIN

H: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

I: PORTAL PROTEIN

J: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

K: PORTAL PROTEIN

L: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

M: PORTAL PROTEIN

N: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

O: PORTAL PROTEIN

P: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

Q: PORTAL PROTEIN

R: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

S: PORTAL PROTEIN

T: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

U: PORTAL PROTEIN

V: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

W: PORTAL PROTEIN

X: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

Y: PORTAL PROTEIN

Z: UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN

hetero molecules

783 kDa, 26 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)	174.314, 221.405, 421.866
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	88 - 139
2	1	1	2	C	88 - 139
3	1	1	2	E	88 - 139
4	1	1	2	G	88 - 139
5	1	1	2	I	88 - 139
6	1	1	2	K	88 - 139
7	1	1	2	M	88 - 139
8	1	1	2	O	88 - 139
9	1	1	2	Q	88 - 139
10	1	1	2	S	88 - 139
11	1	1	2	U	88 - 139
12	1	1	2	W	88 - 139
13	1	1	2	Y	88 - 139
1	2	1	2	A	345 - 466
2	2	1	2	C	345 - 466
3	2	1	2	E	345 - 466
4	2	1	2	G	345 - 466
5	2	1	2	I	345 - 466
6	2	1	2	K	345 - 466
7	2	1	2	M	345 - 466
8	2	1	2	O	345 - 466
9	2	1	2	Q	345 - 466
10	2	1	2	S	345 - 466
11	2	1	2	U	345 - 466
12	2	1	2	W	345 - 466
13	2	1	2	Y	345 - 466
1	1	2	2	A	55 - 87
2	1	2	2	C	55 - 87
3	1	2	2	E	55 - 87
4	1	2	2	G	55 - 87
5	1	2	2	I	55 - 87
6	1	2	2	K	55 - 87
7	1	2	2	M	55 - 87
8	1	2	2	O	55 - 87
9	1	2	2	Q	55 - 87
10	1	2	2	S	55 - 87
11	1	2	2	U	55 - 87
12	1	2	2	W	55 - 87
13	1	2	2	Y	55 - 87
1	2	2	2	A	259 - 344
2	2	2	2	C	259 - 344
3	2	2	2	E	259 - 344
4	2	2	2	G	259 - 344
5	2	2	2	I	259 - 344
6	2	2	2	K	259 - 344
7	2	2	2	M	259 - 344
8	2	2	2	O	259 - 344
9	2	2	2	Q	259 - 344
10	2	2	2	S	259 - 344
11	2	2	2	U	259 - 344
12	2	2	2	W	259 - 344
13	2	2	2	Y	259 - 344
1	3	2	2	A	701 - 801
2	3	2	2	C	701 - 801
3	3	2	2	E	701 - 801
4	3	2	2	G	701 - 801
5	3	2	2	I	701 - 801
6	3	2	2	K	701 - 801
7	3	2	2	M	701 - 801
8	3	2	2	O	701 - 801
9	3	2	2	Q	701 - 801
10	3	2	2	S	701 - 801
11	3	2	2	U	701 - 801
12	3	2	2	W	701 - 801
13	3	2	2	Y	701 - 801
1	1	3	2	A	27 - 54
2	1	3	2	C	27 - 54
3	1	3	2	E	27 - 54
4	1	3	2	G	27 - 54
5	1	3	2	I	27 - 54
6	1	3	2	K	27 - 54
7	1	3	2	M	27 - 54
8	1	3	2	O	27 - 54
9	1	3	2	Q	27 - 54
10	1	3	2	S	27 - 54
11	1	3	2	U	27 - 54
12	1	3	2	W	27 - 54
13	1	3	2	Y	27 - 54
1	2	3	2	A	140 - 169
2	2	3	2	C	140 - 169
3	2	3	2	E	140 - 169
4	2	3	2	G	140 - 169
5	2	3	2	I	140 - 169
6	2	3	2	K	140 - 169
7	2	3	2	M	140 - 169
8	2	3	2	O	140 - 169
9	2	3	2	Q	140 - 169
10	2	3	2	S	140 - 169
11	2	3	2	U	140 - 169
12	2	3	2	W	140 - 169
13	2	3	2	Y	140 - 169
1	3	3	2	A	239 - 258
2	3	3	2	C	239 - 258
3	3	3	2	E	239 - 258
4	3	3	2	G	239 - 258
5	3	3	2	I	239 - 258
6	3	3	2	K	239 - 258
7	3	3	2	M	239 - 258
8	3	3	2	O	239 - 258
9	3	3	2	Q	239 - 258
10	3	3	2	S	239 - 258
11	3	3	2	U	239 - 258
12	3	3	2	W	239 - 258
13	3	3	2	Y	239 - 258
1	1	4	2	B	1 - 30
2	1	4	2	D	1 - 30
3	1	4	2	F	1 - 30
4	1	4	2	H	1 - 30
5	1	4	2	J	1 - 30
6	1	4	2	L	1 - 30
7	1	4	2	N	1 - 30
8	1	4	2	P	1 - 30
9	1	4	2	R	1 - 30
10	1	4	2	T	1 - 30
11	1	4	2	V	1 - 30
12	1	4	2	X	1 - 30
13	1	4	2	Z	1 - 30

NCS ensembles :

ID
1
2
3
4

#1: Protein	PORTAL PROTEIN / PORTAL VERTEX PROTEIN / GP6 Mass: 57405.355 Da / Num. of mol.: 13 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE GENE 6 ALLELE CARRYING MUTATION SIZA (N365K) WAS CLONED FROM THE GENOME OF BACTERIOPHAGE SPP1 SIZA MUTANT Source: (gene. exp.) BACTERIOPHAGE SPP1 (virus) / Variant: SIZA MUTANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54309
#2: Protein/peptide	UNIDENTIFIED FRAGMENT OF PORTAL PROTEIN Mass: 2571.161 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Details: 69 RESIDUE SEGMENTS (FROM 170 TO 238) OF CHAINS A, C, E, G, I, K, M, O, Q, S, U, W, Y ARE PARTIALLY MODELLED BY 30 RESIDUE POLYALANINE SEGMENTS REPRESENTED AS CHAINS B, D, F, H, J, L, N, P, R, T, V, X, Z Source: (gene. exp.) BACTERIOPHAGE SPP1 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical	ChemComp-HG / MERCURY (II) ION / Mercury (element) Mass: 200.590 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Hg
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASN 365 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN E, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN G, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN I, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN K, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN M, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN O, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN Q, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN S, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN U, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN W, ASN 365 TO LYS ENGINEERED RESIDUE IN CHAIN Y, ASN 365 TO LYS

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55 %
Crystal grow	pH: 7.6 Details: 8 MG/ML PORTAL PROTEIN, 20% PEG 400, 100 MM CACL2, 50 MM HEPES PH 7.6, 10% GLYCEROL, 0.5 MM HGCL

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.004
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 1, 2000
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.004 Å / Relative weight: 1
Reflection	Resolution: 3.4→40 Å / Num. obs: 111682 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shell	Resolution: 3.4→3.46 Å / Redundancy: 4 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SIRAS / Resolution: 3.4→39.81 Å / Cor.coef. F_o:F_c: 0.894 / Cor.coef. F_o:F_c free: 0.879 / SU B: 86.295 / SU ML: 0.637 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.319	1121	1 %	RANDOM
R_work	0.288	-	-	-
obs	0.289	110287	100 %	-

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: 134.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.46 Å²	0 Å²	0 Å²
2-	-	5.96 Å²	0 Å²
3-	-	-	-4.5 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→39.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	39234	0	26	0	39260

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	40001
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.137	1.947	54405
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.441	5	5161
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.44	25.18	1807
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.292	15	6123
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.73	15	156
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	6175
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	30732
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	17507
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	27406
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	1184
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.433	0.2	40
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.365	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight position: 0.15

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)
1	1	A	696	tight positional	0.09
1	2	C	696	tight positional	0.08
1	3	E	696	tight positional	0.08
1	4	G	696	tight positional	0.08
1	5	I	696	tight positional	0.09
1	6	K	696	tight positional	0.08
1	7	M	696	tight positional	0.08
1	8	O	696	tight positional	0.08
1	9	Q	696	tight positional	0.09
1	10	S	696	tight positional	0.11
1	11	U	696	tight positional	0.11
1	12	W	696	tight positional	0.09
1	13	Y	696	tight positional	0.09
2	1	A	477	tight positional	0.08
2	2	C	477	tight positional	0.09
2	3	E	477	tight positional	0.09
2	4	G	477	tight positional	0.09
2	5	I	477	tight positional	0.09
2	6	K	477	tight positional	0.09
2	7	M	477	tight positional	0.09
2	8	O	477	tight positional	0.1
2	9	Q	477	tight positional	0.09
2	10	S	477	tight positional	0.11
2	11	U	477	tight positional	0.09
2	12	W	477	tight positional	0.09
2	13	Y	477	tight positional	0.09
3	1	A	304	tight positional	0.08
3	2	C	304	tight positional	0.09
3	3	E	304	tight positional	0.08
3	4	G	304	tight positional	0.08
3	5	I	304	tight positional	0.09
3	6	K	304	tight positional	0.08
3	7	M	304	tight positional	0.08
3	8	O	304	tight positional	0.08
3	9	Q	304	tight positional	0.1
3	10	S	304	tight positional	0.12
3	11	U	304	tight positional	0.13
3	12	W	304	tight positional	0.09
3	13	Y	304	tight positional	0.08
4	1	B	120	tight positional	0.09
4	2	D	120	tight positional	0.07
4	3	F	120	tight positional	0.08
4	4	H	120	tight positional	0.09
4	5	J	120	tight positional	0.11
4	6	L	120	tight positional	0.09
4	7	N	120	tight positional	0.09
4	8	P	120	tight positional	0.1
4	9	R	120	tight positional	0.1
4	10	T	120	tight positional	0.12
4	11	V	120	tight positional	0.14
4	12	X	120	tight positional	0.09
4	13	Z	120	tight positional	0.09
1	1	A	631	medium positional	0.13
1	2	C	631	medium positional	0.11
1	3	E	631	medium positional	0.13
1	4	G	631	medium positional	0.11
1	5	I	631	medium positional	0.12
1	6	K	631	medium positional	0.12
1	7	M	631	medium positional	0.12
1	8	O	631	medium positional	0.12
1	9	Q	631	medium positional	0.13
1	10	S	631	medium positional	0.17
1	11	U	631	medium positional	0.15
1	12	W	631	medium positional	0.12
1	13	Y	631	medium positional	0.12
2	1	A	452	medium positional	0.11
2	2	C	452	medium positional	0.13
2	3	E	452	medium positional	0.12
2	4	G	452	medium positional	0.13
2	5	I	452	medium positional	0.13
2	6	K	452	medium positional	0.13
2	7	M	452	medium positional	0.14
2	8	O	452	medium positional	0.13
2	9	Q	452	medium positional	0.14
2	10	S	452	medium positional	0.15
2	11	U	452	medium positional	0.14
2	12	W	452	medium positional	0.12
2	13	Y	452	medium positional	0.12
3	1	A	305	medium positional	0.11
3	2	C	305	medium positional	0.12
3	3	E	305	medium positional	0.09
3	4	G	305	medium positional	0.11
3	5	I	305	medium positional	0.11
3	6	K	305	medium positional	0.11
3	7	M	305	medium positional	0.1
3	8	O	305	medium positional	0.11
3	9	Q	305	medium positional	0.13
3	10	S	305	medium positional	0.15
3	11	U	305	medium positional	0.17
3	12	W	305	medium positional	0.11
3	13	Y	305	medium positional	0.1
4	1	B	30	medium positional	0.08
4	2	D	30	medium positional	0.08
4	3	F	30	medium positional	0.1
4	4	H	30	medium positional	0.08
4	5	J	30	medium positional	0.11
4	6	L	30	medium positional	0.1
4	7	N	30	medium positional	0.09
4	8	P	30	medium positional	0.1
4	9	R	30	medium positional	0.1
4	10	T	30	medium positional	0.14
4	11	V	30	medium positional	0.12
4	12	X	30	medium positional	0.11
4	13	Z	30	medium positional	0.09

LS refinement shell

Resolution: 3.4→3.49 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.348	95
R_work	0.355	7984

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	3.6291	-0.1496	-0.2716	2.6096	1.0708	1.9641	0.0447	-0.5877	-0.3975	0.4496	-0.1688	0.0383	0.645	0.2248	0.1241	-0.0627	0.085	0.1595	-0.4448	0.6221	-0.9991	114.6734	63.4112	77.573
2	0.0807	0.1232	-0.2782	0.1881	-0.4247	0.9589	0.154	0.8943	0.2466	-0.8029	0.0429	0.0377	-0.515	-0.1472	-0.1969	0.3797	0.2702	0.2111	0.2887	0.1971	-0.0551	115.2279	100.8634	8.7289
3	1.8821	0.058	-0.5254	1.7675	-0.6136	1.6313	0.0745	0.2949	-0.5608	-0.1894	-0.0057	0.6267	0.6328	-0.6636	-0.0688	-0.136	-0.3497	-0.0661	0.0878	-0.1266	-0.2228	72.2454	55.7686	36.2423
4	2.4618	0.0599	-0.3114	2.7128	-0.669	1.0628	0.0008	0.447	-0.9261	-0.1869	-0.0336	0.609	0.8377	-0.4716	0.0328	0.3803	-0.3193	-0.0187	-0.1708	-0.31	-0.1675	89.4299	40.9577	28.3275
5	2.3363	0.6944	-0.1614	3.2555	-0.7561	0.9816	0.0603	0.376	-1.0623	-0.1851	-0.0789	0.1096	0.8712	-0.1238	0.0186	0.5083	0.1529	0.1102	-0.429	-0.2318	-0.1175	112.45	34.833	25.1827
6	2.4175	0.1988	0.0324	3.1739	-0.335	1.2797	0.0933	0.2163	-1.0299	-0.1466	-0.0082	-0.2584	0.8529	0.2143	-0.0851	0.3213	0.4998	0.2263	-0.3707	-0.0162	-0.2662	136.0318	38.7977	27.5282
7	1.9474	0.2078	0.1482	2.8808	-0.2013	1.1486	0.1155	-0.176	-0.6466	0.0529	0.0244	-0.5927	0.6565	0.5173	-0.1398	0.0227	0.6175	0.2522	-0.0561	0.2533	-0.4222	154.7732	51.9435	34.8268
8	2.1865	-0.615	0.787	2.6049	-0.2254	1.6926	0.2303	-0.2859	-0.1977	0.1111	0.0651	-0.6735	0.374	1.0266	-0.2954	-0.4591	0.4014	0.2391	0.4077	0.2175	-0.4234	164.3806	71.2587	45.4063
9	2.5739	-0.5976	1.3628	2.7577	-0.1258	2.4614	0.1941	-0.2236	0.1479	0.3203	0.1037	-0.8707	-0.1065	1.2352	-0.2979	-0.6004	-0.0298	0.2632	0.5068	0.0413	-0.39	162.6531	92.3187	56.8433
10	2.2929	-0.3468	1.3523	1.9711	0.0168	2.8721	0.1347	-0.4295	0.4745	0.3338	0.0903	-0.6469	-0.4726	0.7833	-0.225	-0.2876	-0.4044	0.3841	0.0935	-0.0445	-0.4202	149.9865	110.2987	66.5175
11	2.5557	-0.1687	1.163	1.9233	0.598	3.4851	0.2164	-0.5169	0.7025	0.3613	0.0015	-0.3489	-0.7172	0.4839	-0.2179	-0.0807	-0.3621	0.5347	-0.4857	-0.1093	-0.4473	129.2827	121.0799	72.2128
12	1.7381	0.2197	0.8116	1.4685	0.5582	4.428	0.3254	-0.2348	0.5646	0.1203	-0.1434	0.0892	-0.8311	0.0291	-0.1819	-0.1276	-0.0211	0.6682	-0.8566	0.1014	-0.5203	105.2843	122.1921	72.6244
13	1.6268	-0.5267	-0.5377	1.2133	0.5042	4.1624	0.1253	-0.0622	0.2326	0.0342	-0.0289	0.2443	-0.6402	-0.5488	-0.0964	-0.3608	0.2783	0.4681	-0.5777	0.2962	-0.5382	83.4895	113.3808	67.658
14	2.0238	0.0448	-0.7284	1.5518	0.2789	3.2273	0.2283	0.0152	0.1325	0.0463	-0.2281	0.6562	-0.2206	-0.8364	-0.0002	-0.651	0.2192	0.2241	-0.0565	0.2566	-0.3734	68.8909	96.6646	58.4515
15	1.8726	0.4359	-1.1985	2.1883	-0.2966	2.2182	0.168	0.3765	-0.2168	0.1428	-0.1376	0.8323	0.2033	-0.9364	-0.0305	-0.6282	-0.056	0.0548	0.2835	0.1119	-0.2527	64.833	75.8728	47.1138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	420 - 466
2	X-RAY DIFFRACTION	1	C	420 - 466
3	X-RAY DIFFRACTION	1	E	420 - 466
4	X-RAY DIFFRACTION	1	G	420 - 466
5	X-RAY DIFFRACTION	1	I	420 - 466
6	X-RAY DIFFRACTION	1	K	420 - 466
7	X-RAY DIFFRACTION	1	M	420 - 466
8	X-RAY DIFFRACTION	1	O	420 - 466
9	X-RAY DIFFRACTION	1	Q	420 - 466
10	X-RAY DIFFRACTION	1	S	420 - 466
11	X-RAY DIFFRACTION	1	U	420 - 466
12	X-RAY DIFFRACTION	1	W	420 - 466
13	X-RAY DIFFRACTION	1	Y	420 - 466
14	X-RAY DIFFRACTION	2	A	285 - 320
15	X-RAY DIFFRACTION	2	C	285 - 320
16	X-RAY DIFFRACTION	2	E	285 - 320
17	X-RAY DIFFRACTION	2	G	285 - 320
18	X-RAY DIFFRACTION	2	I	285 - 320
19	X-RAY DIFFRACTION	2	K	285 - 320
20	X-RAY DIFFRACTION	2	M	285 - 320
21	X-RAY DIFFRACTION	2	O	285 - 320
22	X-RAY DIFFRACTION	2	Q	285 - 320
23	X-RAY DIFFRACTION	2	S	285 - 320
24	X-RAY DIFFRACTION	2	U	285 - 320
25	X-RAY DIFFRACTION	2	W	285 - 320
26	X-RAY DIFFRACTION	2	Y	285 - 320
27	X-RAY DIFFRACTION	3	A	27 - 284
28	X-RAY DIFFRACTION	3	A	321 - 419
29	X-RAY DIFFRACTION	3	B	1 - 30
30	X-RAY DIFFRACTION	4	C	27 - 284
31	X-RAY DIFFRACTION	4	C	321 - 419
32	X-RAY DIFFRACTION	4	D	1 - 30
33	X-RAY DIFFRACTION	5	E	27 - 284
34	X-RAY DIFFRACTION	5	E	321 - 419
35	X-RAY DIFFRACTION	5	F	1 - 30
36	X-RAY DIFFRACTION	6	G	27 - 284
37	X-RAY DIFFRACTION	6	G	321 - 419
38	X-RAY DIFFRACTION	6	H	1 - 30
39	X-RAY DIFFRACTION	7	I	27 - 284
40	X-RAY DIFFRACTION	7	I	321 - 419
41	X-RAY DIFFRACTION	7	J	1 - 30
42	X-RAY DIFFRACTION	8	K	27 - 284
43	X-RAY DIFFRACTION	8	K	321 - 419
44	X-RAY DIFFRACTION	8	L	1 - 30
45	X-RAY DIFFRACTION	9	M	27 - 284
46	X-RAY DIFFRACTION	9	M	321 - 419
47	X-RAY DIFFRACTION	9	N	1 - 30
48	X-RAY DIFFRACTION	10	O	27 - 284
49	X-RAY DIFFRACTION	10	O	321 - 419
50	X-RAY DIFFRACTION	10	P	1 - 30
51	X-RAY DIFFRACTION	11	Q	27 - 284
52	X-RAY DIFFRACTION	11	Q	321 - 419
53	X-RAY DIFFRACTION	11	R	1 - 30
54	X-RAY DIFFRACTION	12	S	27 - 284
55	X-RAY DIFFRACTION	12	S	321 - 419
56	X-RAY DIFFRACTION	12	T	1 - 30
57	X-RAY DIFFRACTION	13	U	27 - 284
58	X-RAY DIFFRACTION	13	U	321 - 419
59	X-RAY DIFFRACTION	13	V	1 - 30
60	X-RAY DIFFRACTION	14	W	27 - 284
61	X-RAY DIFFRACTION	14	W	321 - 419
62	X-RAY DIFFRACTION	14	X	1 - 30
63	X-RAY DIFFRACTION	15	Y	27 - 284
64	X-RAY DIFFRACTION	15	Y	321 - 419
65	X-RAY DIFFRACTION	15	Z	1 - 30

-
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