PDB-2jd6: Crystal Structure of the as isolated Ferritin from the Hypertherm...

ID or keywords:

Entry

Database: PDB / ID: 2jd6

Title

Crystal Structure of the as isolated Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus

Components

FERRITIN HOMOLOG

Keywords

METAL TRANSPORT / IRON / PORES / FERRITIN / ARCHAEON / ENTRY CHANNELS / THERMOSTABILITY / HYPERTHERMOPHILE / FERROXIDASE CENTER

Function / homology

Function and homology information

ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
Similarity search - Function

Biological species

PYROCOCCUS FURIOSUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Tatur, J. / Hagen, W.R. / Matias, P.M.

Citation

Journal: J.Biol.Inorg.Chem. / Year: 2007
Title: Crystal Structure of the Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus
Authors: Tatur, J. / Hagen, W.R. / Matias, P.M.

History

Deposition	Jan 5, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

-
Download

PDBx/mmCIF format	2jd6.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb2jd6.ent.gz	1009.7 KB	Display	PDB format
PDBx/mmJSON format	2jd6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2jd6_validation.pdf.gz	569.4 KB	Display	wwPDB validaton report
Full document	2jd6_full_validation.pdf.gz	619.5 KB	Display
Data in XML	2jd6_validation.xml.gz	99 KB	Display
Data in CIF	2jd6_validation.cif.gz	167.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/2jd6 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jd6	HTTPS FTP

-
Related structure data

Related structure data	2jd7C 2jd8C 1vlgS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2jd7-1 2jd7-2 1z4a-2 6ls3-1 2jd8-1 4reu-1 2jd8-2 3kx9-d 5v5k-1 4zl6-1 4ztt-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (7) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

0: FERRITIN HOMOLOG

1: FERRITIN HOMOLOG

2: FERRITIN HOMOLOG

3: FERRITIN HOMOLOG

4: FERRITIN HOMOLOG

5: FERRITIN HOMOLOG

6: FERRITIN HOMOLOG

7: FERRITIN HOMOLOG

8: FERRITIN HOMOLOG

9: FERRITIN HOMOLOG

A: FERRITIN HOMOLOG

B: FERRITIN HOMOLOG

C: FERRITIN HOMOLOG

D: FERRITIN HOMOLOG

E: FERRITIN HOMOLOG

F: FERRITIN HOMOLOG

G: FERRITIN HOMOLOG

H: FERRITIN HOMOLOG

I: FERRITIN HOMOLOG

J: FERRITIN HOMOLOG

K: FERRITIN HOMOLOG

L: FERRITIN HOMOLOG

M: FERRITIN HOMOLOG

N: FERRITIN HOMOLOG

O: FERRITIN HOMOLOG

P: FERRITIN HOMOLOG

Q: FERRITIN HOMOLOG

R: FERRITIN HOMOLOG

S: FERRITIN HOMOLOG

T: FERRITIN HOMOLOG

U: FERRITIN HOMOLOG

V: FERRITIN HOMOLOG

W: FERRITIN HOMOLOG

X: FERRITIN HOMOLOG

Y: FERRITIN HOMOLOG

Z: FERRITIN HOMOLOG

hetero molecules

738 kDa, 36 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

0: FERRITIN HOMOLOG

1: FERRITIN HOMOLOG

2: FERRITIN HOMOLOG

3: FERRITIN HOMOLOG

4: FERRITIN HOMOLOG

5: FERRITIN HOMOLOG

6: FERRITIN HOMOLOG

7: FERRITIN HOMOLOG

8: FERRITIN HOMOLOG

9: FERRITIN HOMOLOG

G: FERRITIN HOMOLOG

H: FERRITIN HOMOLOG

I: FERRITIN HOMOLOG

J: FERRITIN HOMOLOG

K: FERRITIN HOMOLOG

L: FERRITIN HOMOLOG

M: FERRITIN HOMOLOG

N: FERRITIN HOMOLOG

O: FERRITIN HOMOLOG

P: FERRITIN HOMOLOG

Q: FERRITIN HOMOLOG

R: FERRITIN HOMOLOG

Y: FERRITIN HOMOLOG

Z: FERRITIN HOMOLOG

hetero molecules

defined by author&software
492 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: FERRITIN HOMOLOG

B: FERRITIN HOMOLOG

C: FERRITIN HOMOLOG

D: FERRITIN HOMOLOG

E: FERRITIN HOMOLOG

F: FERRITIN HOMOLOG

S: FERRITIN HOMOLOG

T: FERRITIN HOMOLOG

U: FERRITIN HOMOLOG

V: FERRITIN HOMOLOG

W: FERRITIN HOMOLOG

X: FERRITIN HOMOLOG

hetero molecules

A: FERRITIN HOMOLOG

B: FERRITIN HOMOLOG

C: FERRITIN HOMOLOG

D: FERRITIN HOMOLOG

E: FERRITIN HOMOLOG

F: FERRITIN HOMOLOG

S: FERRITIN HOMOLOG

T: FERRITIN HOMOLOG

U: FERRITIN HOMOLOG

V: FERRITIN HOMOLOG

W: FERRITIN HOMOLOG

X: FERRITIN HOMOLOG

hetero molecules

defined by author&software
492 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	254.097, 341.422, 265.524
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:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 1

Dom-ID	Component-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	A	K	17	17
2	1	GLU	GLU	B	L	17	17
3	1	GLU	GLU	C	M	17	17
4	1	GLU	GLU	D	N	17	17
5	1	GLU	GLU	E	O	17	17
6	1	GLU	GLU	F	P	17	17
7	1	GLU	GLU	G	Q	17	17
8	1	GLU	GLU	H	R	17	17
9	1	GLU	GLU	I	S	17	17
10	1	GLU	GLU	J	T	17	17
11	1	GLU	GLU	K	U	17	17
12	1	GLU	GLU	L	V	17	17
13	1	GLU	GLU	M	W	17	17
14	1	GLU	GLU	N	X	17	17
15	1	GLU	GLU	O	Y	17	17
16	1	GLU	GLU	P	Z	17	17
17	1	GLU	GLU	Q	AA	17	17
18	1	GLU	GLU	R	BA	17	17
19	3	GLU	GLU	S - 1	CA - B	17	17
20	3	GLU	GLU	T	DA	17	17
21	3	GLU	GLU	U	EA	17	17
22	3	GLU	GLU	V	FA	17	17
23	3	GLU	GLU	W	GA	17	17
24	3	GLU	GLU	X	HA	17	17
25	3	GLU	GLU	Y	IA	17	17
26	3	GLU	GLU	Z	JA	17	17
27	3	GLU	GLU	0	A	17	17
28	3	GLU	GLU	1 - J	B - T	17	17
29	3	GLU	GLU	2 - K	C - U	17	17
30	3	GLU	GLU	3 - L	D - V	17	17
31	3	GLU	GLU	4 - M	E - W	17	17
32	3	GLU	GLU	5 - N	F - X	17	17
33	3	GLU	GLU	6 - O	G - Y	17	17
34	3	GLU	GLU	7 - P	H - Z	17	17
35	3	GLU	GLU	8 - Q	I - AA	17	17
36	3	GLU	GLU	9 - R	J - BA	17	17
1	2	HIS	HIS	A	K	50 - 53	50 - 53
2	2	HIS	HIS	B	L	50 - 53	50 - 53
3	2	HIS	HIS	C	M	50 - 53	50 - 53
4	2	HIS	HIS	D	N	50 - 53	50 - 53
5	2	HIS	HIS	E	O	50 - 53	50 - 53
6	2	HIS	HIS	F	P	50 - 53	50 - 53
7	2	HIS	HIS	G	Q	50 - 53	50 - 53
8	2	HIS	HIS	H	R	50 - 53	50 - 53
9	2	HIS	HIS	I	S	50 - 53	50 - 53
10	2	HIS	HIS	J	T	50 - 53	50 - 53
11	2	HIS	HIS	K	U	50 - 53	50 - 53
12	2	HIS	HIS	L	V	50 - 53	50 - 53
13	2	HIS	HIS	M	W	50 - 53	50 - 53
14	2	HIS	HIS	N	X	50 - 53	50 - 53
15	2	HIS	HIS	O	Y	50 - 53	50 - 53
16	2	HIS	HIS	P	Z	50 - 53	50 - 53
17	2	HIS	HIS	Q	AA	50 - 53	50 - 53
18	2	HIS	HIS	R	BA	50 - 53	50 - 53
19	4	HIS	HIS	S	CA	50 - 53	50 - 53
20	4	HIS	HIS	T	DA	50 - 53	50 - 53
21	4	HIS	HIS	U	EA	50 - 53	50 - 53
22	4	HIS	HIS	V	FA	50 - 53	50 - 53
23	4	HIS	HIS	W	GA	50 - 53	50 - 53
24	4	HIS	HIS	X	HA	50 - 53	50 - 53
25	4	HIS	HIS	Y	IA	50 - 53	50 - 53
26	4	HIS	HIS	Z	JA	50 - 53	50 - 53
27	4	HIS	HIS	0	A	50 - 53	50 - 53
28	4	HIS	HIS	1	B	50 - 53	50 - 53
29	4	HIS	HIS	2	C	50 - 53	50 - 53
30	4	HIS	HIS	3	D	50 - 53	50 - 53
31	4	HIS	HIS	4	E	50 - 53	50 - 53
32	4	HIS	HIS	5	F	50 - 53	50 - 53
33	4	HIS	HIS	6	G	50 - 53	50 - 53
34	4	HIS	HIS	7	H	50 - 53	50 - 53
35	4	HIS	HIS	8	I	50 - 53	50 - 53
36	4	HIS	HIS	9	J	50 - 53	50 - 53

#1: Protein	... FERRITIN HOMOLOG / FERRITIN Mass: 20333.123 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8U2T8
#2: Chemical	... ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	EACH CHAIN CONTAINS TWO MONOMERS WITH GIVEN SEQUENCE.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4 Å³/Da / Density % sol: 69.2 %
Crystal grow	Details: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 ...Details: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION.

Crystal

Density Matthews: 4 Å³/Da / Density % sol: 69.2 %

Crystal grow

Details: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 24, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7712 Å / Relative weight: 1
Reflection	Resolution: 2.75→58.2 Å / Num. obs: 295335 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / R_merge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.75→2.9 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.3 / Mean I/σ(I) obs: 3.1 / % possible all: 97.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.3.0021	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VLG

1vlg

Resolution: 2.75→204.12 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.881 / SU B: 9.832 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY FOR C-TERMINAL RESIDUES BEYOND 167 (667) WAS NOT VISIBLE.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	14914	5.1 %	RANDOM
R_work	0.195	-	-	-
obs	0.198	280375	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 33.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.91 Å²	0 Å²	0 Å²
2-	-	-0.92 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→204.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	49788	0	236	790	50814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	51218
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.432	1.98	69016
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.337	5	5978
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.842	24.732	2665
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.611	15	9361
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.328	15	252
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	6985
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	39284
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	25079
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	35029
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	1854
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	0.208	0.2	138
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.186	0.2	20
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	2.074	3	30939
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.252	4.5	47994
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.778	6	23593
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.098	9	21021
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

Ens-ID: 1 / Number: 80 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.08	0.1
2	B	tight positional	0.08	0.1
3	C	tight positional	0.08	0.1
4	D	tight positional	0.08	0.1
5	E	tight positional	0.08	0.1
6	F	tight positional	0.08	0.1
7	G	tight positional	0.08	0.1
8	H	tight positional	0.08	0.1
9	I	tight positional	0.08	0.1
10	J	tight positional	0.08	0.1
11	K	tight positional	0.08	0.1
12	L	tight positional	0.08	0.1
13	M	tight positional	0.08	0.1
14	N	tight positional	0.08	0.1
15	O	tight positional	0.08	0.1
16	P	tight positional	0.08	0.1
17	Q	tight positional	0.08	0.1
18	R	tight positional	0.08	0.1
19	S	tight positional	0.08	0.1
20	T	tight positional	0.08	0.1
21	U	tight positional	0.08	0.1
22	V	tight positional	0.08	0.1
23	W	tight positional	0.08	0.1
24	X	tight positional	0.08	0.1
25	Y	tight positional	0.08	0.1
26	Z	tight positional	0.08	0.1
27	0	tight positional	0.08	0.1
28	1	tight positional	0.08	0.1
29	2	tight positional	0.08	0.1
30	3	tight positional	0.08	0.1
31	4	tight positional	0.08	0.1
32	5	tight positional	0.08	0.1
33	6	tight positional	0.08	0.1
34	7	tight positional	0.08	0.1
35	8	tight positional	0.08	0.1
36	9	tight positional	0.08	0.1
1	A	tight thermal	0.58	1
2	B	tight thermal	0.55	0.01
3	C	tight thermal	0.52	0
4	D	tight thermal	0.56	0
5	E	tight thermal	0.75	0
6	F	tight thermal	0.54	0
7	G	tight thermal	0.56	0
8	H	tight thermal	0.76	0
9	I	tight thermal	0.33	0
10	J	tight thermal	0.41	0
11	K	tight thermal	0.37	0
12	L	tight thermal	0.38	0
13	M	tight thermal	0.58	0
14	N	tight thermal	0.5	0
15	O	tight thermal	0.75	0
16	P	tight thermal	0.64	0
17	Q	tight thermal	0.45	0
18	R	tight thermal	0.53	0
19	S	tight thermal	0.58	1
20	T	tight thermal	0.55	0.01
21	U	tight thermal	0.52	0
22	V	tight thermal	0.56	0
23	W	tight thermal	0.75	0
24	X	tight thermal	0.54	0
25	Y	tight thermal	0.56	0
26	Z	tight thermal	0.76	0
27	0	tight thermal	0.33	0
28	1	tight thermal	0.41	0
29	2	tight thermal	0.37	0
30	3	tight thermal	0.38	0
31	4	tight thermal	0.58	0
32	5	tight thermal	0.5	0
33	6	tight thermal	0.75	0
34	7	tight thermal	0.64	0
35	8	tight thermal	0.45	0
36	9	tight thermal	0.53	0

LS refinement shell

Resolution: 2.75→2.82 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.339	1028
R_work	0.276	19977

-
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