PDB-4a5m: Redox regulator HypR in its oxidized form

ID or keywords:

Entry

Database: PDB / ID: 4a5m

Title

Redox regulator HypR in its oxidized form

Components

UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

Keywords

TRANSCRIPTION / ACTIVATOR / DNA-BINDING

Function / homology

Function and homology information

Biological species

BACILLUS SUBTILIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Palm, G.J. / Waack, P. / Read, R.J. / Hinrichs, W.

Citation

Journal: Nucleic Acids Res. / Year: 2012
Title: Structural Insights Into the Redox-Switch Mechanism of the Marr/Duf24-Type Regulator Hypr
Authors: Palm, G.J. / Chi, B.K. / Waack, P. / Gronau, K. / Becher, D. / Albrecht, D. / Hinrichs, W. / Read, R.J. / Antelmann, H.

History

Deposition	Oct 26, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2012	Group: Other
Revision 1.2	May 23, 2012	Group: Other
Revision 1.3	May 1, 2024	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 / 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 / _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
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	4a5nC C: citing same article (ref.)
Similar structure data	2hzt-1 1ub9-1 2fsw-d 4a5n-1 3f6z-2 4a5n-2 2nz7-d 6fnn-1 2pqu-1 6fno-2 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

4a5nC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

B: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

C: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

D: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

E: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

F: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

G: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

H: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

hetero molecules

125 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

B: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

hetero molecules

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

2

C: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

D: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

hetero molecules

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

3

E: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

F: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

hetero molecules

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

4

G: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

H: UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR

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

Unit cell

Length a, b, c (Å)	82.851, 82.851, 354.436
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	14 - 108	14 - 108
2	1	ARG	ARG	B	B	14 - 108	14 - 108
1	2	ASP	ASP	A	A	14 - 109	14 - 109
2	2	ASP	ASP	C	C	14 - 109	14 - 109
1	3	ARG	ARG	A	A	14 - 108	14 - 108
2	3	ARG	ARG	D	D	14 - 108	14 - 108
1	4	ASP	ASP	A	A	14 - 109	14 - 109
2	4	ASP	ASP	E	E	14 - 109	14 - 109
1	5	ARG	ARG	A	A	14 - 108	14 - 108
2	5	ARG	ARG	F	F	14 - 108	14 - 108
1	6	ASP	ASP	A	A	14 - 109	14 - 109
2	6	ASP	ASP	G	G	14 - 109	14 - 109
1	7	ARG	ARG	A	A	14 - 108	14 - 108
2	7	ARG	ARG	H	H	14 - 108	14 - 108
1	8	ARG	ARG	B	B	14 - 108	14 - 108
2	8	ARG	ARG	C	C	14 - 108	14 - 108
1	9	VAL	VAL	B	B	14 - 110	14 - 110
2	9	VAL	VAL	D	D	14 - 110	14 - 110
1	10	ARG	ARG	B	B	14 - 108	14 - 108
2	10	ARG	ARG	E	E	14 - 108	14 - 108
1	11	VAL	VAL	B	B	14 - 110	14 - 110
2	11	VAL	VAL	F	F	14 - 110	14 - 110
1	12	ARG	ARG	B	B	14 - 108	14 - 108
2	12	ARG	ARG	G	G	14 - 108	14 - 108
1	13	VAL	VAL	B	B	14 - 110	14 - 110
2	13	VAL	VAL	H	H	14 - 110	14 - 110
1	14	ARG	ARG	C	C	14 - 108	14 - 108
2	14	ARG	ARG	D	D	14 - 108	14 - 108
1	15	ASP	ASP	C	C	14 - 109	14 - 109
2	15	ASP	ASP	E	E	14 - 109	14 - 109
1	16	ARG	ARG	C	C	14 - 108	14 - 108
2	16	ARG	ARG	F	F	14 - 108	14 - 108
1	17	ASP	ASP	C	C	14 - 109	14 - 109
2	17	ASP	ASP	G	G	14 - 109	14 - 109
1	18	ARG	ARG	C	C	14 - 108	14 - 108
2	18	ARG	ARG	H	H	14 - 108	14 - 108
1	19	ARG	ARG	D	D	14 - 108	14 - 108
2	19	ARG	ARG	E	E	14 - 108	14 - 108
1	20	VAL	VAL	D	D	14 - 110	14 - 110
2	20	VAL	VAL	F	F	14 - 110	14 - 110
1	21	ARG	ARG	D	D	14 - 108	14 - 108
2	21	ARG	ARG	G	G	14 - 108	14 - 108
1	22	VAL	VAL	D	D	14 - 110	14 - 110
2	22	VAL	VAL	H	H	14 - 110	14 - 110
1	23	ARG	ARG	E	E	14 - 108	14 - 108
2	23	ARG	ARG	F	F	14 - 108	14 - 108
1	24	ASP	ASP	E	E	14 - 109	14 - 109
2	24	ASP	ASP	G	G	14 - 109	14 - 109
1	25	ARG	ARG	E	E	14 - 108	14 - 108
2	25	ARG	ARG	H	H	14 - 108	14 - 108
1	26	ARG	ARG	F	F	14 - 108	14 - 108
2	26	ARG	ARG	G	G	14 - 108	14 - 108
1	27	VAL	VAL	F	F	14 - 110	14 - 110
2	27	VAL	VAL	H	H	14 - 110	14 - 110
1	28	ARG	ARG	G	G	14 - 108	14 - 108
2	28	ARG	ARG	H	H	14 - 108	14 - 108

NCS ensembles :
NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.99944, -0.00817, -0.03259), (0.03106, 0.14549, -0.98887), (0.01282, -0.98933, -0.14515)	48.65292, 4.48964, 5.61245
2	given	(-0.41638, -0.21258, -0.88399), (-0.89777, 0.24976, 0.36281), (0.14366, 0.94469, -0.29484)	60.22563, 8.93466, 3.6509
3	given	(0.45705, 0.26996, 0.84748), (-0.23628, -0.88174, 0.40829), (0.85749, -0.38685, -0.33921)	-11.22959, 0.5928, -2.54031
4	given	(-0.50187, -0.86481, 0.01517), (-0.86492, 0.50163, -0.01694), (0.00704, -0.02163, -0.99974)	-1.02367, -0.4187, -0.07218
5	given	(0.51915, 0.85437, 0.02328), (-0.15311, 0.06617, 0.98599), (0.84086, -0.51544, 0.16517)	49.76716, 4.28215, 5.67271
6	given	(0.39043, 0.27666, 0.87808), (0.22322, 0.89687, -0.38184), (-0.89316, 0.34508, 0.28841)	60.63821, 8.90535, 3.58599
7	given	(-0.44506, -0.26979, -0.8539), (0.889, -0.24784, -0.38504), (-0.10775, -0.93048, 0.35015)	-11.76844, 1.57208, -3.18622

#1: Protein	UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR / REDOX REGULATOR HYPR Mass: 15582.888 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: TRPC2 / Plasmid: PDGHYPR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37486
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	ETHYLENE GLYCOL (EDO): PRECIPITANT COMPONENT CHLORIDE ION (CL): BUFFER COMPONENT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 %
Crystal grow	pH: 7.5 Details: 6% PEG 8000 0.4 M LI2SO4, CRYOPROTECTANT 15% PEG8000, 15% PEG 400, pH 7.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.918

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2011 / Details: MIRRORS

Radiation

Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.918 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.554
1	1	K, H, -L	2	0.446

Reflection

Resolution: 3→45.6 Å / Num. obs: 24764 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / B_iso Wilson estimate: 82 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 14.92

Reflection shell

Resolution: 3→3.18 Å / Redundancy: 4.6 % / R_merge(I) obs: 1.09 / Mean I/σ(I) obs: 1.38 / % possible all: 77.4

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 3→45.61 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.909 / SU B: 16.76 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24966	1238	5 %	RANDOM
R_work	0.20749	-	-	-
obs	0.20965	23432	89.83 %	-

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: 107.596 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.44 Å²	0 Å²	0 Å²
2-	-	1.44 Å²	0 Å²
3-	-	-	-2.88 Å²

Refinement step

Cycle: LAST / Resolution: 3→45.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6408	0	37	24	6469

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	6595
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	4785
X-RAY DIFFRACTION	r_angle_refined_deg	1.732	1.963	8874
X-RAY DIFFRACTION	r_angle_other_deg	1.803	3.003	11527
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.951	5	764
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.517	22.84	324
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.83	15	1224
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.034	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	944
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	7108
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1420
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
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3761	0.09
1	2	B	3761	0.09
2	1	A	3871	0.07
2	2	C	3871	0.07
3	1	A	3760	0.1
3	2	D	3760	0.1
4	1	A	3863	0.08
4	2	E	3863	0.08
5	1	A	3760	0.08
5	2	F	3760	0.08
6	1	A	3860	0.07
6	2	G	3860	0.07
7	1	A	3703	0.11
7	2	H	3703	0.11
8	1	B	3776	0.09
8	2	C	3776	0.09
9	1	B	3839	0.09
9	2	D	3839	0.09
10	1	B	3757	0.09
10	2	E	3757	0.09
11	1	B	3890	0.06
11	2	F	3890	0.06
12	1	B	3769	0.1
12	2	G	3769	0.1
13	1	B	3720	0.11
13	2	H	3720	0.11
14	1	C	3776	0.1
14	2	D	3776	0.1
15	1	C	3899	0.05
15	2	E	3899	0.05
16	1	C	3771	0.09
16	2	F	3771	0.09
17	1	C	3901	0.05
17	2	G	3901	0.05
18	1	C	3702	0.11
18	2	H	3702	0.11
19	1	D	3791	0.09
19	2	E	3791	0.09
20	1	D	3842	0.08
20	2	F	3842	0.08
21	1	D	3757	0.11
21	2	G	3757	0.11
22	1	D	3694	0.13
22	2	H	3694	0.13
23	1	E	3755	0.09
23	2	F	3755	0.09
24	1	E	3888	0.06
24	2	G	3888	0.06
25	1	E	3689	0.12
25	2	H	3689	0.12
26	1	F	3765	0.09
26	2	G	3765	0.09
27	1	F	3727	0.11
27	2	H	3727	0.11
28	1	G	3686	0.12
28	2	H	3686	0.12

LS refinement shell

Resolution: 2.998→3.076 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.308	78	-
R_work	0.254	1415	-
obs	-	-	73.62 %

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	3.0914	1.6568	0.0273	2.4448	0.8759	0.7536	-0.2023	0.0155	-0.259	-0.1762	0.1713	-0.295	0.1104	0.0897	0.031	0.1388	-0.0569	0.0659	0.1561	-0.0358	0.1247	14.5065	-0.2193	-5.6105
2	4.7768	-1.3074	1.6097	1.2529	0.37	2.5519	-0.3657	0.0798	-0.2071	0.0194	0.4604	-0.3697	-0.3665	0.3167	-0.0947	0.0676	-0.0626	-0.0378	0.3795	-0.1189	0.5326	33.7291	10.8337	7.3597
3	4.939	0.9792	0.857	2.9712	-0.718	0.6952	-0.0604	0.3055	0.1329	-0.2712	-0.189	-0.817	0.2914	0.1662	0.2493	0.2117	0.0842	0.0368	0.3409	0.0316	0.2839	25.9332	-1.3865	39.8304
4	0.9121	-1.6032	-1.1867	3.9561	0.6563	4.5589	0.3867	0.1337	0.3685	-0.5383	0.0014	-0.6158	-0.4923	-0.4055	-0.388	0.2134	0.0447	0.1519	0.3906	0.0182	0.2185	9.2643	8.8778	22.6117
5	1.8074	0.1246	0.4169	0.9258	-0.3419	0.8504	-0.0339	-0.1384	-0.2224	-0.0403	0.0214	0.1872	0.0391	0.1168	0.0125	0.0861	-0.0413	-0.0175	0.1898	0.0457	0.1297	-7.9926	-13.2055	5.8569
6	0.8604	0.4382	1.2223	4.705	0.3284	1.8511	0.1306	-0.2657	-0.2199	-0.3124	0.0259	0.103	0.0684	-0.3518	-0.1565	0.2455	-0.1621	-0.1535	0.2087	-0.0151	0.5236	-27.206	-24.4996	-7.108
7	3.9693	-0.3194	-0.1059	3.5133	1.4697	1.3897	-0.2268	-0.2973	-0.5516	0.463	-0.0243	0.6847	0.4783	0.1379	0.2512	0.3694	-0.0334	0.0694	0.1059	0.0269	0.2908	-11.7649	-24.1825	-39.6804
8	2.9688	-1.7148	1.2264	2.2048	-1.2189	5.7221	-0.2141	-0.2416	-0.4606	0.4148	0.3975	0.6941	-0.5526	-0.4611	-0.1834	0.3763	-0.0811	0.1237	0.2208	0.1003	0.248	-13.0178	-4.4335	-22.7576

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 109
2	X-RAY DIFFRACTION	2	B	14 - 109
3	X-RAY DIFFRACTION	3	C	14 - 109
4	X-RAY DIFFRACTION	4	D	14 - 109
5	X-RAY DIFFRACTION	5	E	14 - 109
6	X-RAY DIFFRACTION	6	F	14 - 109
7	X-RAY DIFFRACTION	7	G	14 - 109
8	X-RAY DIFFRACTION	8	H	14 - 109

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