PDB-5xgo: The Ferritin E-Domain: Toward Understanding Its Role in Protein C...

ID or keywords:

Entry

Database: PDB / ID: 5xgo

Title

The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the Crystal Structure of a Maxi-/Mini-Ferritin Chimera

Components

DNA protection during starvation protein,Bacterioferritin

Keywords

OXIDOREDUCTASE /

Ferritin /

Protein engineering / protein cage

Function / homology

Function and homology information

DnaA-Dps complex /

Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions /

nucleoid / chromosome condensation / response to starvation /

ferroxidase / intracellular sequestering of iron ion /

ferroxidase activity / negative regulation of DNA-templated DNA replication initiation ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.99 Å

Authors

Cornell, T.A. / Srivastava, Y. / Jauch, R. / Fan, R. / Orner, B.P.

Funding support

Singapore, 1items

Citation

Journal: Biochemistry / Year: 2017
Title: The Crystal Structure of a Maxi/Mini-Ferritin Chimera Reveals Guiding Principles for the Assembly of Protein Cages.
Authors: Cornell, T.A. / Srivastava, Y. / Jauch, R. / Fan, R. / Orner, B.P.

History

Deposition	Apr 14, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5xgo.cif.gz	756.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5xgo.ent.gz	624.1 KB	Display	PDB format
PDBx/mmJSON format	5xgo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/5xgo ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xgo	HTTPS FTP

-
Related structure data

Similar structure data	6zgl-d 6gcm-2 6qvx-1 1f30-1 1l8i-d 6gcm-1 1dps-d 1jts-1 6qvx-2 4dyu-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	#35 - Nov 2002 Ferritin and Transferrin similarity (7) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: DNA protection during starvation protein,Bacterioferritin

B: DNA protection during starvation protein,Bacterioferritin

C: DNA protection during starvation protein,Bacterioferritin

D: DNA protection during starvation protein,Bacterioferritin

E: DNA protection during starvation protein,Bacterioferritin

F: DNA protection during starvation protein,Bacterioferritin

G: DNA protection during starvation protein,Bacterioferritin

H: DNA protection during starvation protein,Bacterioferritin

I: DNA protection during starvation protein,Bacterioferritin

J: DNA protection during starvation protein,Bacterioferritin

K: DNA protection during starvation protein,Bacterioferritin

L: DNA protection during starvation protein,Bacterioferritin

hetero molecules

272 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	103.139, 104.723, 207.756
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	1	LEU	LEU	ASP	ASP	B	B	14 - 167	28 - 181
1	2	LEU	LEU	LEU	LEU	A	A	14 - 168	28 - 182
2	2	LEU	LEU	LEU	LEU	C	C	14 - 168	28 - 182
1	3	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	3	LEU	LEU	ASP	ASP	D	D	14 - 167	28 - 181
1	4	LEU	LEU	LEU	LEU	A	A	14 - 168	28 - 182
2	4	LEU	LEU	LEU	LEU	E	E	14 - 168	28 - 182
1	5	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	5	LEU	LEU	ASP	ASP	F	F	14 - 167	28 - 181
1	6	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	6	LEU	LEU	ASP	ASP	G	G	14 - 167	28 - 181
1	7	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	7	LEU	LEU	ASP	ASP	H	H	14 - 167	28 - 181
1	8	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	8	LEU	LEU	ASP	ASP	I	I	14 - 167	28 - 181
1	9	LEU	LEU	LEU	LEU	A	A	14 - 168	28 - 182
2	9	LEU	LEU	LEU	LEU	J	J	14 - 168	28 - 182
1	10	LEU	LEU	ASP	ASP	A	A	14 - 167	28 - 181
2	10	LEU	LEU	ASP	ASP	K	K	14 - 167	28 - 181
1	11	LEU	LEU	LEU	LEU	A	A	14 - 168	28 - 182
2	11	LEU	LEU	LEU	LEU	L	L	14 - 168	28 - 182
1	12	LEU	LEU	ASP	ASP	B	B	14 - 167	28 - 181
2	12	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
1	13	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	13	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
1	14	LEU	LEU	ASP	ASP	B	B	14 - 167	28 - 181
2	14	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
1	15	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	15	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
1	16	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	16	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
1	17	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	17	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
1	18	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	18	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
1	19	LEU	LEU	ASP	ASP	B	B	14 - 167	28 - 181
2	19	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	20	ASN	ASN	LEU	LEU	B	B	13 - 168	27 - 182
2	20	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	21	LEU	LEU	ASP	ASP	B	B	14 - 167	28 - 181
2	21	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	22	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	22	LEU	LEU	ASP	ASP	D	D	14 - 167	28 - 181
1	23	LEU	LEU	LEU	LEU	C	C	14 - 168	28 - 182
2	23	LEU	LEU	LEU	LEU	E	E	14 - 168	28 - 182
1	24	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	24	LEU	LEU	ASP	ASP	F	F	14 - 167	28 - 181
1	25	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	25	LEU	LEU	ASP	ASP	G	G	14 - 167	28 - 181
1	26	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	26	LEU	LEU	ASP	ASP	H	H	14 - 167	28 - 181
1	27	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	27	LEU	LEU	ASP	ASP	I	I	14 - 167	28 - 181
1	28	LEU	LEU	LEU	LEU	C	C	14 - 168	28 - 182
2	28	LEU	LEU	LEU	LEU	J	J	14 - 168	28 - 182
1	29	LEU	LEU	ASP	ASP	C	C	14 - 167	28 - 181
2	29	LEU	LEU	ASP	ASP	K	K	14 - 167	28 - 181
1	30	LEU	LEU	LEU	LEU	C	C	14 - 168	28 - 182
2	30	LEU	LEU	LEU	LEU	L	L	14 - 168	28 - 182
1	31	LEU	LEU	ASP	ASP	D	D	14 - 167	28 - 181
2	31	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
1	32	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
2	32	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
1	33	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
2	33	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
1	34	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
2	34	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
1	35	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
2	35	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
1	36	LEU	LEU	ASP	ASP	D	D	14 - 167	28 - 181
2	36	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	37	ASN	ASN	LEU	LEU	D	D	13 - 168	27 - 182
2	37	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	38	LEU	LEU	ASP	ASP	D	D	14 - 167	28 - 181
2	38	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	39	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
2	39	LEU	LEU	ASP	ASP	F	F	14 - 167	28 - 181
1	40	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
2	40	LEU	LEU	ASP	ASP	G	G	14 - 167	28 - 181
1	41	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
2	41	LEU	LEU	ASP	ASP	H	H	14 - 167	28 - 181
1	42	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
2	42	LEU	LEU	ASP	ASP	I	I	14 - 167	28 - 181
1	43	LEU	LEU	LEU	LEU	E	E	14 - 168	28 - 182
2	43	LEU	LEU	LEU	LEU	J	J	14 - 168	28 - 182
1	44	LEU	LEU	ASP	ASP	E	E	14 - 167	28 - 181
2	44	LEU	LEU	ASP	ASP	K	K	14 - 167	28 - 181
1	45	LEU	LEU	LEU	LEU	E	E	14 - 168	28 - 182
2	45	LEU	LEU	LEU	LEU	L	L	14 - 168	28 - 182
1	46	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
2	46	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
1	47	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
2	47	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
1	48	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
2	48	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
1	49	LEU	LEU	ASP	ASP	F	F	14 - 167	28 - 181
2	49	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	50	ASN	ASN	LEU	LEU	F	F	13 - 168	27 - 182
2	50	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	51	LEU	LEU	ASP	ASP	F	F	14 - 167	28 - 181
2	51	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	52	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
2	52	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
1	53	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
2	53	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
1	54	LEU	LEU	ASP	ASP	G	G	14 - 167	28 - 181
2	54	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	55	ASN	ASN	LEU	LEU	G	G	13 - 168	27 - 182
2	55	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	56	LEU	LEU	ASP	ASP	G	G	14 - 167	28 - 181
2	56	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	57	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
2	57	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
1	58	LEU	LEU	ASP	ASP	H	H	14 - 167	28 - 181
2	58	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	59	ASN	ASN	LEU	LEU	H	H	13 - 168	27 - 182
2	59	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	60	LEU	LEU	ASP	ASP	H	H	14 - 167	28 - 181
2	60	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	61	LEU	LEU	ASP	ASP	I	I	14 - 167	28 - 181
2	61	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
1	62	ASN	ASN	LEU	LEU	I	I	13 - 168	27 - 182
2	62	ASN	ASN	LEU	LEU	K	K	13 - 168	27 - 182
1	63	LEU	LEU	ASP	ASP	I	I	14 - 167	28 - 181
2	63	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181
1	64	LEU	LEU	ASP	ASP	J	J	14 - 167	28 - 181
2	64	LEU	LEU	ASP	ASP	K	K	14 - 167	28 - 181
1	65	LEU	LEU	LEU	LEU	J	J	14 - 168	28 - 182
2	65	LEU	LEU	LEU	LEU	L	L	14 - 168	28 - 182
1	66	LEU	LEU	ASP	ASP	K	K	14 - 167	28 - 181
2	66	LEU	LEU	ASP	ASP	L	L	14 - 167	28 - 181

NCS ensembles :

#1: Protein	DNA protection during starvation protein,Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557 Mass: 22658.719 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: Chimera protein of residues 1-163 from DNA protection during starvation protein (P0ABT2) and residues 138-158 from Bacterioferritin (P0ABD3). Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dps, pexB, vtm, b0812, JW0797, bfr, b3336, JW3298 / Plasmid: pET-46 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABT2, UniProt: P0ABD3, Oxidoreductases; Oxidizing metal ions, ferroxidase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1781 / 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: 2.06 Å³/Da / Density % sol: 40.38 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion / pH: 4.2 / Details: 0.2M lithium sulphate, 18% PEG 1000, pH 4.2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.99→50 Å / Num. obs: 135428 / % possible obs: 92.3 % / Redundancy: 12.8 % / R_merge(I) obs: 0.069 / Net I/σ(I): 320.3
Reflection shell	Highest resolution: 2 Å / R_merge(I) obs: 0.517

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 1.99→46.76 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.946 / SU B: 7.259 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20721	7156	5 %	RANDOM
R_work	0.17929	-	-	-
obs	0.18069	135428	92.33 %	-

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: 33.276 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.67 Å²	-0 Å²	0 Å²
2-	-	0.57 Å²	-0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: 1 / Resolution: 1.99→46.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14780	0	2	1781	16563

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	14996
X-RAY DIFFRACTION	r_bond_other_d	0.013	0.02	14634
X-RAY DIFFRACTION	r_angle_refined_deg	1.88	1.951	20321
X-RAY DIFFRACTION	r_angle_other_deg	1.921	3	33499
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.021	5	1855
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.547	24.966	739
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.874	15	2695
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.359	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.183	0.2	2407
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	16999
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	3393
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.487	2.131	7456
X-RAY DIFFRACTION	r_mcbond_other	1.485	2.131	7455
X-RAY DIFFRACTION	r_mcangle_it	2.062	3.181	9299
X-RAY DIFFRACTION	r_mcangle_other	2.063	3.181	9300
X-RAY DIFFRACTION	r_scbond_it	2.668	2.461	7540
X-RAY DIFFRACTION	r_scbond_other	2.668	2.461	7541
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.182	3.563	11023
X-RAY DIFFRACTION	r_long_range_B_refined	18.355	20.189	19564
X-RAY DIFFRACTION	r_long_range_B_other	18.355	20.19	19565
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	19304	0.04
1	2	B	19304	0.04
2	1	A	19612	0.04
2	2	C	19612	0.04
3	1	A	19468	0.04
3	2	D	19468	0.04
4	1	A	19380	0.04
4	2	E	19380	0.04
5	1	A	19494	0.04
5	2	F	19494	0.04
6	1	A	19410	0.03
6	2	G	19410	0.03
7	1	A	19382	0.04
7	2	H	19382	0.04
8	1	A	19212	0.05
8	2	I	19212	0.05
9	1	A	19540	0.04
9	2	J	19540	0.04
10	1	A	19326	0.04
10	2	K	19326	0.04
11	1	A	19392	0.04
11	2	L	19392	0.04
12	1	B	19218	0.04
12	2	C	19218	0.04
13	1	B	19486	0.04
13	2	D	19486	0.04
14	1	B	19346	0.04
14	2	E	19346	0.04
15	1	B	19458	0.05
15	2	F	19458	0.05
16	1	B	19378	0.05
16	2	G	19378	0.05
17	1	B	19354	0.05
17	2	H	19354	0.05
18	1	B	19244	0.05
18	2	I	19244	0.05
19	1	B	19210	0.04
19	2	J	19210	0.04
20	1	B	19310	0.05
20	2	K	19310	0.05
21	1	B	19364	0.04
21	2	L	19364	0.04
22	1	C	19524	0.03
22	2	D	19524	0.03
23	1	C	19302	0.05
23	2	E	19302	0.05
24	1	C	19400	0.05
24	2	F	19400	0.05
25	1	C	19352	0.04
25	2	G	19352	0.04
26	1	C	19360	0.03
26	2	H	19360	0.03
27	1	C	19264	0.04
27	2	I	19264	0.04
28	1	C	19590	0.04
28	2	J	19590	0.04
29	1	C	19346	0.05
29	2	K	19346	0.05
30	1	C	19326	0.05
30	2	L	19326	0.05
31	1	D	19190	0.04
31	2	E	19190	0.04
32	1	D	19624	0.04
32	2	F	19624	0.04
33	1	D	19590	0.04
33	2	G	19590	0.04
34	1	D	19576	0.04
34	2	H	19576	0.04
35	1	D	19522	0.04
35	2	I	19522	0.04
36	1	D	19488	0.02
36	2	J	19488	0.02
37	1	D	19566	0.04
37	2	K	19566	0.04
38	1	D	19218	0.04
38	2	L	19218	0.04
39	1	E	19258	0.04
39	2	F	19258	0.04
40	1	E	19166	0.05
40	2	G	19166	0.05
41	1	E	19080	0.05
41	2	H	19080	0.05
42	1	E	18988	0.05
42	2	I	18988	0.05
43	1	E	19320	0.04
43	2	J	19320	0.04
44	1	E	19076	0.04
44	2	K	19076	0.04
45	1	E	19516	0.04
45	2	L	19516	0.04
46	1	F	19600	0.04
46	2	G	19600	0.04
47	1	F	19524	0.05
47	2	H	19524	0.05
48	1	F	19404	0.05
48	2	I	19404	0.05
49	1	F	19396	0.04
49	2	J	19396	0.04
50	1	F	19526	0.04
50	2	K	19526	0.04
51	1	F	19272	0.04
51	2	L	19272	0.04
52	1	G	19508	0.04
52	2	H	19508	0.04
53	1	G	19378	0.05
53	2	I	19378	0.05
54	1	G	19314	0.04
54	2	J	19314	0.04
55	1	G	19400	0.05
55	2	K	19400	0.05
56	1	G	19238	0.04
56	2	L	19238	0.04
57	1	H	19612	0.05
57	2	I	19612	0.05
58	1	H	19254	0.05
58	2	J	19254	0.05
59	1	H	19374	0.05
59	2	K	19374	0.05
60	1	H	19104	0.05
60	2	L	19104	0.05
61	1	I	19364	0.03
61	2	J	19364	0.03
62	1	I	19330	0.05
62	2	K	19330	0.05
63	1	I	19082	0.05
63	2	L	19082	0.05
64	1	J	19316	0.04
64	2	K	19316	0.04
65	1	J	19414	0.04
65	2	L	19414	0.04
66	1	K	19090	0.04
66	2	L	19090	0.04

LS refinement shell

Resolution: 1.99→2.042 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	559	-
R_work	0.228	10162	-
obs	-	-	95 %

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	0.1442	0.0869	-0.1954	0.2837	0.0391	0.4194	-0.0181	0.0284	0.058	-0.0277	0.0394	0.092	-0.0198	0.0025	-0.0213	0.1046	0.0245	0.005	0.0528	0.0255	0.0966	2.206	17.276	11.583
2	0.3962	0.0727	0.1193	0.2125	0.0733	0.1622	0.0502	-0.0156	0.0653	0.0085	0.0007	-0.0047	-0.0697	0.0347	-0.0509	0.1173	-0.0276	0.0202	0.0431	-0.0019	0.1017	28.974	30.672	22.467
3	0.3775	0.3183	-0.1034	0.3834	-0.1254	0.2924	0.0369	0.0039	0.0652	0.1223	0.0044	0.0649	-0.015	-0.0029	-0.0414	0.1774	-0.0047	0.0582	0.0163	-0.0246	0.0675	7.554	18.843	42.949
4	0.3764	-0.0685	0.0232	0.2369	-0.1028	0.1297	-0.082	0.0032	-0.0206	-0.0219	0.013	-0.0272	0.1328	-0.0179	0.0691	0.2264	-0.0133	0.0616	0.0063	-0.0158	0.071	12.639	-28.762	23.295
5	0.1831	0.0795	-0.1702	0.2591	0.0175	0.2571	-0.038	0.0491	0.0239	-0.0036	0.0339	0.0878	0.0458	-0.0193	0.0041	0.1114	-0.0164	0.002	0.0597	-0.0029	0.0735	-3.048	-3.996	10.772
6	0.1205	0.069	-0.1055	0.4234	-0.1629	0.2993	-0.0583	0.0671	-0.0083	-0.0891	0.0437	-0.0588	0.0919	-0.0212	0.0146	0.1586	-0.0138	0.0622	0.055	-0.0174	0.0664	23.916	-14.284	-2.792
7	0.1357	0.0206	0.0708	0.2687	-0.0758	0.1319	0.0124	0.0075	-0.0046	-0.0552	-0.012	-0.0837	-0.0192	0.0094	-0.0004	0.0655	-0.0142	0.0382	0.0617	0.016	0.1248	42.984	19.756	9.528
8	0.3886	0.0348	-0.0414	0.2434	0.0247	0.0592	-0.0085	0.0191	-0.0025	0.176	-0.0378	0.0134	0.0961	0.0085	0.0463	0.2786	-0.0101	0.0433	0.0139	0.0092	0.0448	12.918	-21.633	44.008
9	0.0794	0.0677	-0.0028	0.6646	0.005	0.1728	-0.0322	0.0385	-0.0511	-0.0529	0.0334	-0.1904	0.0657	0.0415	-0.0012	0.1084	0.0285	0.1014	0.0402	0.001	0.1558	44.553	-11.676	4.211
10	0.217	0.183	-0.1755	0.4337	-0.0089	0.215	0.0313	-0.1077	-0.1881	0.1599	-0.1501	-0.2416	0.0205	0.0469	0.1188	0.1868	0.0152	-0.1083	0.0958	0.0902	0.2025	43.78	-13.585	45.05
11	0.2582	0.2137	0.0423	0.4446	0.0899	0.1592	0.0389	-0.054	0.0479	0.2256	-0.0245	-0.0219	0.0442	0.0371	-0.0145	0.2446	-0.0234	-0.0209	0.0342	-0.0222	0.0261	21.556	6.993	55.003
12	0.0249	0.0859	-0.056	0.5266	0.0611	0.4188	0.0195	-0.0311	-0.0597	0.0936	-0.091	-0.2564	-0.0362	0.082	0.0714	0.057	0.014	-0.0724	0.0862	0.0399	0.1841	54.684	0.303	31.959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 168
2	X-RAY DIFFRACTION	2	B	13 - 168
3	X-RAY DIFFRACTION	3	C	14 - 168
4	X-RAY DIFFRACTION	4	D	13 - 168
5	X-RAY DIFFRACTION	5	E	14 - 168
6	X-RAY DIFFRACTION	6	F	13 - 168
7	X-RAY DIFFRACTION	7	G	13 - 168
8	X-RAY DIFFRACTION	8	H	13 - 168
9	X-RAY DIFFRACTION	9	I	13 - 168
10	X-RAY DIFFRACTION	10	J	14 - 168
11	X-RAY DIFFRACTION	11	K	13 - 168
12	X-RAY DIFFRACTION	12	L	14 - 168

-
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