PDB-5lnh: Structure of full length Unliganded CodY from Bacillus subtilis

ID or keywords:

Entry

Database: PDB / ID: 5lnh

Title

Structure of full length Unliganded CodY from Bacillus subtilis

Components

GTP-sensing transcriptional pleiotropic repressor CodY

Keywords

TRANSCRIPTION / GAF / wHTH / transcriptional regulator / CodY

Function / homology

Function and homology information

DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / GTP binding / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Wilkinson, A.J. / Levdikov, V.M. / Blagova, E.V.

Funding support

United Kingdom,

United States, 3items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council	BBS/B1213X	United Kingdom
Wellcome Trust	082829/Z/07/Z	United Kingdom
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	GM042219	United States

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Structure of the Branched-chain Amino Acid and GTP-sensing Global Regulator, CodY, from Bacillus subtilis.
Authors: Levdikov, V.M. / Blagova, E. / Young, V.L. / Belitsky, B.R. / Lebedev, A. / Sonenshein, A.L. / Wilkinson, A.J.

History

Deposition	Aug 4, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2017	Group: Database references
Revision 1.2	Aug 30, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 30, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4	Jan 10, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5lnh.cif.gz	487.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5lnh.ent.gz	405.2 KB	Display	PDB format
PDBx/mmJSON format	5lnh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5lnh_validation.pdf.gz	500.3 KB	Display	wwPDB validaton report
Full document	5lnh_full_validation.pdf.gz	604.3 KB	Display
Data in XML	5lnh_validation.xml.gz	61.5 KB	Display
Data in CIF	5lnh_validation.cif.gz	88.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ln/5lnh ftp://data.pdbj.org/pub/pdb/validation_reports/ln/5lnh	HTTPS FTP

-
Related structure data

Related structure data	5loeC 5lojC 5looC 2b0lS 2gx5S 2b18 2hgv S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5loj-d 5loo-5 5loo-6 5loo-7 5loo-4 5loo-8 5loo-1 6ddp-d 5loo-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1)

Deposited unit

A: GTP-sensing transcriptional pleiotropic repressor CodY

B: GTP-sensing transcriptional pleiotropic repressor CodY

C: GTP-sensing transcriptional pleiotropic repressor CodY

D: GTP-sensing transcriptional pleiotropic repressor CodY

E: GTP-sensing transcriptional pleiotropic repressor CodY

F: GTP-sensing transcriptional pleiotropic repressor CodY

G: GTP-sensing transcriptional pleiotropic repressor CodY

H: GTP-sensing transcriptional pleiotropic repressor CodY

I: GTP-sensing transcriptional pleiotropic repressor CodY

K: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

300 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-sensing transcriptional pleiotropic repressor CodY

H: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GTP-sensing transcriptional pleiotropic repressor CodY

G: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: GTP-sensing transcriptional pleiotropic repressor CodY

F: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: GTP-sensing transcriptional pleiotropic repressor CodY

E: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

I: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

K: GTP-sensing transcriptional pleiotropic repressor CodY

hetero molecules

defined by software
60.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.869, 110.550, 257.414
Angle α, β, γ (deg.)	90.00, 91.30, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

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	SER	SER	PHE	PHE	A	A	37 - 135	36 - 134
2	1	SER	SER	PHE	PHE	B	B	37 - 135	36 - 134
3	1	SER	SER	PHE	PHE	C	C	37 - 135	36 - 134
4	1	SER	SER	PHE	PHE	D	D	37 - 135	36 - 134
5	1	SER	SER	PHE	PHE	E	E	37 - 135	36 - 134
6	1	SER	SER	PHE	PHE	F	F	37 - 135	36 - 134
7	1	SER	SER	PHE	PHE	G	G	37 - 135	36 - 134
8	1	SER	SER	PHE	PHE	H	H	37 - 135	36 - 134
9	1	SER	SER	PHE	PHE	I	I	37 - 135	36 - 134
10	1	SER	SER	PHE	PHE	K	J	37 - 135	36 - 134
1	2	ASN	ASN	VAL	VAL	A	A	136 - 150	135 - 149
2	2	ASN	ASN	VAL	VAL	B	B	136 - 150	135 - 149
3	2	ASN	ASN	VAL	VAL	C	C	136 - 150	135 - 149
4	2	ASN	ASN	VAL	VAL	D	D	136 - 150	135 - 149
5	2	ASN	ASN	VAL	VAL	E	E	136 - 150	135 - 149
6	2	ASN	ASN	VAL	VAL	F	F	136 - 150	135 - 149
7	2	ASN	ASN	VAL	VAL	G	G	136 - 150	135 - 149
8	2	ASN	ASN	VAL	VAL	H	H	136 - 150	135 - 149
9	2	ASN	ASN	VAL	VAL	I	I	136 - 150	135 - 149
10	2	ASN	ASN	VAL	VAL	K	J	136 - 150	135 - 149
1	3	GLY	GLY	LEU	LEU	A	A	151 - 179	150 - 178
2	3	GLY	GLY	LEU	LEU	B	B	151 - 179	150 - 178
3	3	GLY	GLY	LEU	LEU	C	C	151 - 179	150 - 178
4	3	GLY	GLY	LEU	LEU	D	D	151 - 179	150 - 178
5	3	GLY	GLY	LEU	LEU	E	E	151 - 179	150 - 178
6	3	GLY	GLY	LEU	LEU	F	F	151 - 179	150 - 178
7	3	GLY	GLY	LEU	LEU	G	G	151 - 179	150 - 178
8	3	GLY	GLY	LEU	LEU	H	H	151 - 179	150 - 178
9	3	GLY	GLY	LEU	LEU	I	I	151 - 179	150 - 178
10	3	GLY	GLY	LEU	LEU	K	J	151 - 179	150 - 178
1	4	SER	SER	LEU	LEU	A	A	180 - 256	179 - 255
2	4	SER	SER	LEU	LEU	B	B	180 - 256	179 - 255
3	4	SER	SER	LEU	LEU	C	C	180 - 256	179 - 255
4	4	SER	SER	LEU	LEU	D	D	180 - 256	179 - 255
5	4	SER	SER	LEU	LEU	E	E	180 - 256	179 - 255
6	4	SER	SER	LEU	LEU	F	F	180 - 256	179 - 255
7	4	SER	SER	LEU	LEU	G	G	180 - 256	179 - 255
8	4	SER	SER	LEU	LEU	H	H	180 - 256	179 - 255
9	4	SER	SER	LEU	LEU	I	I	180 - 256	179 - 255
10	4	SER	SER	LEU	LEU	K	J	180 - 256	179 - 255
1	5	ALA	ALA	ASP	ASP	A	A	2 - 36	1 - 35
2	5	ALA	ALA	ASP	ASP	B	B	2 - 36	1 - 35
3	5	ALA	ALA	ASP	ASP	C	C	2 - 36	1 - 35
4	5	ALA	ALA	ASP	ASP	D	D	2 - 36	1 - 35
5	5	ALA	ALA	ASP	ASP	E	E	2 - 36	1 - 35
6	5	ALA	ALA	ASP	ASP	F	F	2 - 36	1 - 35
7	5	ALA	ALA	ASP	ASP	G	G	2 - 36	1 - 35
8	5	ALA	ALA	ASP	ASP	H	H	2 - 36	1 - 35
9	5	ALA	ALA	ASP	ASP	I	I	2 - 36	1 - 35
10	5	ALA	ALA	ASP	ASP	K	J	2 - 36	1 - 35

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	GTP-sensing transcriptional pleiotropic repressor CodY / Vegetative protein 286B / VEG286B Mass: 29932.975 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: codY, BSU16170 / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: P39779
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.34 Å³/Da / Density % sol: 63.13 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M sodium citrate pH 5.6, 20 mM Tris-HCl pH 7.5, 35 % ammonium sulphate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9782 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003 / Details: mirror
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9782 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 57358 / % possible obs: 72 % / Redundancy: 3.2 % / R_merge(I) obs: 0.102 / Net I/σ(I): 18.3
Reflection shell	Resolution: 3→3.11 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.51

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2GX5, 2B0L

2gx5

2b0l

Resolution: 3→46.68 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.904 / SU ML: 0.471 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27936	2880	5.1 %	RANDOM
R_work	0.23038	-	-	-
obs	0.23279	53946	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 86.521 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.45 Å²	0 Å²	0.87 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	-0.1 Å²

Refinement step

Cycle: 1 / Resolution: 3→46.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20020	0	60	10	20090

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	20268
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.607	1.988	27302
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.222	5	2540
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.97	25.208	960
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.963	15	3920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.872	15	150
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	3200
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	14880
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.266	0.2	11654
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	14460
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	916
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	0.309	0.2	147
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	8
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	0.615	1.5	12902
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.79	2	20370
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.313	3	7975
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.96	4.5	6932
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	396	tight positional	0.06	0.05
1	2	B	396	tight positional	0.06	0.05
1	3	C	396	tight positional	0.04	0.05
1	4	D	396	tight positional	0.04	0.05
1	5	E	396	tight positional	0.05	0.05
1	6	F	396	tight positional	0.04	0.05
1	7	G	396	tight positional	0.04	0.05
1	8	H	396	tight positional	0.04	0.05
1	9	I	396	tight positional	0.05	0.05
1	10	K	396	tight positional	0.04	0.05
2	1	A	60	tight positional	0.05	0.05
2	2	B	60	tight positional	0.06	0.05
2	3	C	60	tight positional	0.05	0.05
2	4	D	60	tight positional	0.04	0.05
2	5	E	60	tight positional	0.04	0.05
2	6	F	60	tight positional	0.04	0.05
2	7	G	60	tight positional	0.06	0.05
2	8	H	60	tight positional	0.04	0.05
2	9	I	60	tight positional	0.05	0.05
2	10	K	60	tight positional	0.04	0.05
3	1	A	116	tight positional	0.07	0.05
3	2	B	116	tight positional	0.08	0.05
3	3	C	116	tight positional	0.05	0.05
3	4	D	116	tight positional	0.05	0.05
3	5	E	116	tight positional	0.05	0.05
3	6	F	116	tight positional	0.05	0.05
3	7	G	116	tight positional	0.07	0.05
3	8	H	116	tight positional	0.06	0.05
3	9	I	116	tight positional	0.05	0.05
3	10	K	116	tight positional	0.05	0.05
4	1	A	308	tight positional	0.05	0.05
4	2	B	308	tight positional	0.06	0.05
4	3	C	308	tight positional	0.04	0.05
4	4	D	308	tight positional	0.04	0.05
4	5	E	308	tight positional	0.05	0.05
4	6	F	308	tight positional	0.06	0.05
4	7	G	308	tight positional	0.05	0.05
4	8	H	308	tight positional	0.05	0.05
4	9	I	308	tight positional	0.04	0.05
4	10	K	308	tight positional	0.04	0.05
5	1	A	140	tight positional	0.06	0.05
5	2	B	140	tight positional	0.06	0.05
5	3	C	140	tight positional	0.05	0.05
5	4	D	140	tight positional	0.05	0.05
5	5	E	140	tight positional	0.06	0.05
5	6	F	140	tight positional	0.05	0.05
5	7	G	140	tight positional	0.07	0.05
5	8	H	140	tight positional	0.05	0.05
5	9	I	140	tight positional	0.06	0.05
5	10	K	140	tight positional	0.05	0.05
1	1	A	402	medium positional	0.73	0.5
1	2	B	402	medium positional	0.63	0.5
1	3	C	402	medium positional	0.56	0.5
1	4	D	402	medium positional	0.67	0.5
1	5	E	402	medium positional	0.6	0.5
1	6	F	402	medium positional	0.69	0.5
1	7	G	402	medium positional	0.64	0.5
1	8	H	402	medium positional	0.62	0.5
1	9	I	402	medium positional	0.7	0.5
1	10	K	402	medium positional	0.58	0.5
2	1	A	52	medium positional	0.56	0.5
2	2	B	52	medium positional	0.43	0.5
2	3	C	52	medium positional	0.62	0.5
2	4	D	52	medium positional	0.47	0.5
2	5	E	52	medium positional	0.44	0.5
2	6	F	52	medium positional	0.5	0.5
2	7	G	52	medium positional	0.43	0.5
2	8	H	52	medium positional	0.54	0.5
2	9	I	52	medium positional	0.45	0.5
2	10	K	52	medium positional	0.38	0.5
3	1	A	108	medium positional	0.85	0.5
3	2	B	108	medium positional	0.75	0.5
3	3	C	108	medium positional	0.76	0.5
3	4	D	108	medium positional	0.83	0.5
3	5	E	108	medium positional	0.69	0.5
3	6	F	108	medium positional	0.71	0.5
3	7	G	108	medium positional	0.85	0.5
3	8	H	108	medium positional	0.81	0.5
3	9	I	108	medium positional	0.65	0.5
3	10	K	108	medium positional	0.76	0.5
4	1	A	290	medium positional	0.74	0.5
4	2	B	290	medium positional	0.77	0.5
4	3	C	290	medium positional	0.68	0.5
4	4	D	290	medium positional	0.73	0.5
4	5	E	290	medium positional	0.8	0.5
4	6	F	290	medium positional	0.74	0.5
4	7	G	290	medium positional	0.65	0.5
4	8	H	290	medium positional	0.83	0.5
4	9	I	290	medium positional	0.71	0.5
4	10	K	290	medium positional	0.69	0.5
5	1	A	130	medium positional	0.66	0.5
5	2	B	130	medium positional	0.63	0.5
5	3	C	130	medium positional	0.63	0.5
5	4	D	130	medium positional	0.75	0.5
5	5	E	130	medium positional	0.62	0.5
5	6	F	130	medium positional	0.54	0.5
5	7	G	130	medium positional	0.63	0.5
5	8	H	130	medium positional	0.68	0.5
5	9	I	130	medium positional	0.67	0.5
5	10	K	130	medium positional	0.64	0.5
1	1	A	396	tight thermal	0.09	0.5
1	2	B	396	tight thermal	0.09	0.5
1	3	C	396	tight thermal	0.04	0.5
1	4	D	396	tight thermal	0.05	0.5
1	5	E	396	tight thermal	0.06	0.5
1	6	F	396	tight thermal	0.03	0.5
1	7	G	396	tight thermal	0.06	0.5
1	8	H	396	tight thermal	0.04	0.5
1	9	I	396	tight thermal	0.07	0.5
1	10	K	396	tight thermal	0.05	0.5
2	1	A	60	tight thermal	0.08	0.5
2	2	B	60	tight thermal	0.09	0.5
2	3	C	60	tight thermal	0.06	0.5
2	4	D	60	tight thermal	0.06	0.5
2	5	E	60	tight thermal	0.1	0.5
2	6	F	60	tight thermal	0.06	0.5
2	7	G	60	tight thermal	0.09	0.5
2	8	H	60	tight thermal	0.06	0.5
2	9	I	60	tight thermal	0.09	0.5
2	10	K	60	tight thermal	0.06	0.5
3	1	A	116	tight thermal	0.1	0.5
3	2	B	116	tight thermal	0.1	0.5
3	3	C	116	tight thermal	0.07	0.5
3	4	D	116	tight thermal	0.08	0.5
3	5	E	116	tight thermal	0.11	0.5
3	6	F	116	tight thermal	0.09	0.5
3	7	G	116	tight thermal	0.1	0.5
3	8	H	116	tight thermal	0.09	0.5
3	9	I	116	tight thermal	0.09	0.5
3	10	K	116	tight thermal	0.08	0.5
4	1	A	308	tight thermal	0.07	0.5
4	2	B	308	tight thermal	0.08	0.5
4	3	C	308	tight thermal	0.05	0.5
4	4	D	308	tight thermal	0.04	0.5
4	5	E	308	tight thermal	0.06	0.5
4	6	F	308	tight thermal	0.06	0.5
4	7	G	308	tight thermal	0.06	0.5
4	8	H	308	tight thermal	0.07	0.5
4	9	I	308	tight thermal	0.05	0.5
4	10	K	308	tight thermal	0.05	0.5
5	1	A	140	tight thermal	0.09	0.5
5	2	B	140	tight thermal	0.07	0.5
5	3	C	140	tight thermal	0.05	0.5
5	4	D	140	tight thermal	0.06	0.5
5	5	E	140	tight thermal	0.08	0.5
5	6	F	140	tight thermal	0.05	0.5
5	7	G	140	tight thermal	0.09	0.5
5	8	H	140	tight thermal	0.08	0.5
5	9	I	140	tight thermal	0.09	0.5
5	10	K	140	tight thermal	0.06	0.5
1	1	A	402	medium thermal	0.7	2
1	2	B	402	medium thermal	0.7	2
1	3	C	402	medium thermal	0.37	2
1	4	D	402	medium thermal	0.38	2
1	5	E	402	medium thermal	0.51	2
1	6	F	402	medium thermal	0.37	2
1	7	G	402	medium thermal	0.49	2
1	8	H	402	medium thermal	0.36	2
1	9	I	402	medium thermal	0.48	2
1	10	K	402	medium thermal	0.36	2
2	1	A	52	medium thermal	0.63	2
2	2	B	52	medium thermal	0.55	2
2	3	C	52	medium thermal	0.39	2
2	4	D	52	medium thermal	0.56	2
2	5	E	52	medium thermal	0.55	2
2	6	F	52	medium thermal	0.5	2
2	7	G	52	medium thermal	0.65	2
2	8	H	52	medium thermal	0.41	2
2	9	I	52	medium thermal	0.77	2
2	10	K	52	medium thermal	0.38	2
3	1	A	108	medium thermal	1.33	2
3	2	B	108	medium thermal	1.32	2
3	3	C	108	medium thermal	0.78	2
3	4	D	108	medium thermal	0.79	2
3	5	E	108	medium thermal	0.76	2
3	6	F	108	medium thermal	1.03	2
3	7	G	108	medium thermal	1.11	2
3	8	H	108	medium thermal	0.82	2
3	9	I	108	medium thermal	0.76	2
3	10	K	108	medium thermal	0.95	2
4	1	A	290	medium thermal	0.54	2
4	2	B	290	medium thermal	0.72	2
4	3	C	290	medium thermal	0.51	2
4	4	D	290	medium thermal	0.46	2
4	5	E	290	medium thermal	0.47	2
4	6	F	290	medium thermal	0.51	2
4	7	G	290	medium thermal	0.51	2
4	8	H	290	medium thermal	0.53	2
4	9	I	290	medium thermal	0.38	2
4	10	K	290	medium thermal	0.36	2
5	1	A	130	medium thermal	0.83	2
5	2	B	130	medium thermal	0.68	2
5	3	C	130	medium thermal	0.64	2
5	4	D	130	medium thermal	0.58	2
5	5	E	130	medium thermal	0.91	2
5	6	F	130	medium thermal	0.52	2
5	7	G	130	medium thermal	0.94	2
5	8	H	130	medium thermal	0.56	2
5	9	I	130	medium thermal	0.81	2
5	10	K	130	medium thermal	0.45	2

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.439	53	-
R_work	0.425	837	-
obs	-	-	100 %

-
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://pdbjlvh1.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