PDB-2f4i: Crystal structure of an ob-fold protein (tm0957) from thermotoga ...

ID or keywords:

Entry

Database: PDB / ID: 2f4i

Title

Crystal structure of an ob-fold protein (tm0957) from thermotoga maritima msb8 at 1.90 A resolution

Components

hypothetical protein TM0957

Keywords

UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function and homology information

Envelope glycoprotein gp160, DUF2291, helical domain / Envelope glycoprotein gp160, DUF2291, alpha/beta domain / Uncharacterised conserved protein UCP033535, periplasmic lipoprotein / TM0957-like superfamily / Predicted periplasmic lipoprotein (DUF2291) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.25 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of hypothetical protein (tm0957) from THERMOTOGA MARITIMA at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Nov 23, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 7, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE 1. THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] ...

Remark 300

BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2f4i.cif.gz	166.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2f4i.ent.gz	138.5 KB	Display	PDB format
PDBx/mmJSON format	2f4i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2f4i_validation.pdf.gz	482.6 KB	Display	wwPDB validaton report
Full document	2f4i_full_validation.pdf.gz	495.5 KB	Display
Data in XML	2f4i_validation.xml.gz	35 KB	Display
Data in CIF	2f4i_validation.cif.gz	49.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4i ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4i	HTTPS FTP

-
Related structure data

Similar structure data	5bnd-3 5bnd-2 5bnd-1 5emv-1 3pvv-1 3hnr-d 5hx4-1 4tjw-2 6h5u-2 6nv6-3 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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 358444

Similar structure data

Other databases

TargetDB: 358444

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein TM0957

B: hypothetical protein TM0957

C: hypothetical protein TM0957

D: hypothetical protein TM0957

hetero molecules

92.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: hypothetical protein TM0957

hetero molecules

defined by author
Evidence: gel filtration, light scattering
23.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: hypothetical protein TM0957

hetero molecules

defined by author
Evidence: gel filtration, light scattering
23.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: hypothetical protein TM0957

hetero molecules

defined by author&software
Evidence: gel filtration, light scattering
23.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: hypothetical protein TM0957

defined by author&software
Evidence: gel filtration, light scattering
23.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: hypothetical protein TM0957

hetero molecules

B: hypothetical protein TM0957

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.677, 78.075, 82.487
Angle α, β, γ (deg.)	90.00, 93.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	LEU	C	C	39 - 60	19 - 40
2	1	PHE	LEU	A	A	39 - 60	19 - 40
3	1	PHE	LEU	B	B	39 - 60	19 - 40
4	1	PHE	LEU	D	D	39 - 60	19 - 40
1	2	GLY	VAL	C	C	61 - 86	41 - 66
2	2	GLY	VAL	A	A	61 - 86	41 - 66
3	2	GLY	VAL	B	B	61 - 86	41 - 66
4	2	GLY	VAL	D	D	61 - 86	41 - 66
1	3	ARG	HIS	C	C	92 - 128	72 - 108
2	3	ARG	HIS	A	A	92 - 128	72 - 108
3	3	ARG	HIS	B	B	92 - 128	72 - 108
4	3	ARG	HIS	D	D	92 - 128	72 - 108
1	4	GLY	ALA	C	C	133 - 156	113 - 136
2	4	GLY	ALA	A	A	133 - 156	113 - 136
3	4	GLY	ALA	B	B	133 - 156	113 - 136
4	4	GLY	ALA	D	D	133 - 156	113 - 136
1	5	THR	GLN	C	C	157 - 214	137 - 194
2	5	THR	GLN	A	A	157 - 214	137 - 194
3	5	THR	GLN	B	B	157 - 214	137 - 194
4	5	THR	GLN	D	D	157 - 214	137 - 194

NCS ensembles :

ID
1
2
3
4
5

Details

SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

#1: Protein	hypothetical protein TM0957 Mass: 23160.959 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0957 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X052
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.41 Å³/Da / Density % sol: 48.61 %
Crystal grow	Temperature: 277 K / pH: 8.5 Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97942, 0.95372

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2005 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY

Radiation

Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97942	1
2	0.95372	1

Reflection

Resolution: 2.25→29.83 Å / Num. obs: 39599 / % possible obs: 100 % / Redundancy: 3.8 % / R_merge(I) obs: 0.09 / R_sym value: 0.09 / Net I/σ(I): 5.8

Reflection shell

Resolution: 2.25→2.37 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Phasing

Phasing	Method: MAD

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SCALA		data scaling
PDB_EXTRACT	1.601	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHELX		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.25→29.83 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.912 / SU B: 12.66 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	1987	5 %	RANDOM
R_work	0.19	-	-	-
all	0.193	-	-	-
obs	0.19279	37581	99.8 %	-

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: 15.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.41 Å²	0 Å²	-0.16 Å²
2-	-	0.79 Å²	0 Å²
3-	-	-	-1.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→29.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5639	0	4	484	6127

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	5866
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3947
X-RAY DIFFRACTION	r_angle_refined_deg	1.562	1.971	7942
X-RAY DIFFRACTION	r_angle_other_deg	1.039	3	9686
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.912	5	705
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.041	25.122	287
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.485	15.078	1086
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.295	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	925
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6408
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1153
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	1022
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	3962
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2775
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	3173
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	353
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.091	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.101	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.175	0.2	28
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.267	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.195	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.707	3	3715
X-RAY DIFFRACTION	r_mcbond_other	0.38	3	1442
X-RAY DIFFRACTION	r_mcangle_it	2.336	5	5748
X-RAY DIFFRACTION	r_scbond_it	1.169	2	2526
X-RAY DIFFRACTION	r_scangle_it	1.611	3	2194

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	C	123	tight positional	0.04	0.05
1	2	A	123	tight positional	0.07	0.05
1	3	B	123	tight positional	0.07	0.05
1	4	D	123	tight positional	0.06	0.05
2	1	C	154	tight positional	0.04	0.05
2	2	A	154	tight positional	0.06	0.05
2	3	B	154	tight positional	0.05	0.05
2	4	D	154	tight positional	0.06	0.05
3	1	C	218	tight positional	0.05	0.05
3	2	A	218	tight positional	0.06	0.05
3	3	B	218	tight positional	0.07	0.05
3	4	D	218	tight positional	0.05	0.05
4	1	C	142	tight positional	0.07	0.05
4	2	A	142	tight positional	0.09	0.05
4	3	B	142	tight positional	0.12	0.05
4	4	D	142	tight positional	0.05	0.05
5	1	C	341	tight positional	0.05	0.05
5	2	A	341	tight positional	0.06	0.05
5	3	B	341	tight positional	0.06	0.05
5	4	D	341	tight positional	0.06	0.05
1	1	C	184	medium positional	0.56	0.5
1	2	A	184	medium positional	0.28	0.5
1	3	B	184	medium positional	0.42	0.5
1	4	D	184	medium positional	0.37	0.5
2	1	C	140	medium positional	0.2	0.5
2	2	A	140	medium positional	0.33	0.5
2	3	B	140	medium positional	0.34	0.5
2	4	D	140	medium positional	0.38	0.5
3	1	C	266	medium positional	0.35	0.5
3	2	A	266	medium positional	0.42	0.5
3	3	B	266	medium positional	0.4	0.5
3	4	D	266	medium positional	0.42	0.5
4	1	C	110	medium positional	0.68	0.5
4	2	A	110	medium positional	0.84	0.5
4	3	B	110	medium positional	0.76	0.5
4	4	D	110	medium positional	0.7	0.5
5	1	C	357	medium positional	0.5	0.5
5	2	A	357	medium positional	0.72	0.5
5	3	B	357	medium positional	0.58	0.5
5	4	D	357	medium positional	0.56	0.5
1	1	C	123	tight thermal	0.18	0.5
1	2	A	123	tight thermal	0.2	0.5
1	3	B	123	tight thermal	0.16	0.5
1	4	D	123	tight thermal	0.17	0.5
2	1	C	154	tight thermal	0.16	0.5
2	2	A	154	tight thermal	0.18	0.5
2	3	B	154	tight thermal	0.18	0.5
2	4	D	154	tight thermal	0.13	0.5
3	1	C	218	tight thermal	0.17	0.5
3	2	A	218	tight thermal	0.16	0.5
3	3	B	218	tight thermal	0.17	0.5
3	4	D	218	tight thermal	0.18	0.5
4	1	C	142	tight thermal	0.2	0.5
4	2	A	142	tight thermal	0.19	0.5
4	3	B	142	tight thermal	0.18	0.5
4	4	D	142	tight thermal	0.14	0.5
5	1	C	341	tight thermal	0.18	0.5
5	2	A	341	tight thermal	0.17	0.5
5	3	B	341	tight thermal	0.17	0.5
5	4	D	341	tight thermal	0.14	0.5
1	1	C	184	medium thermal	0.74	2
1	2	A	184	medium thermal	0.96	2
1	3	B	184	medium thermal	0.77	2
1	4	D	184	medium thermal	0.68	2
2	1	C	140	medium thermal	0.54	2
2	2	A	140	medium thermal	0.99	2
2	3	B	140	medium thermal	0.86	2
2	4	D	140	medium thermal	0.78	2
3	1	C	266	medium thermal	0.61	2
3	2	A	266	medium thermal	0.6	2
3	3	B	266	medium thermal	0.56	2
3	4	D	266	medium thermal	0.74	2
4	1	C	110	medium thermal	1.04	2
4	2	A	110	medium thermal	1.03	2
4	3	B	110	medium thermal	1.04	2
4	4	D	110	medium thermal	0.5	2
5	1	C	357	medium thermal	0.73	2
5	2	A	357	medium thermal	0.74	2
5	3	B	357	medium thermal	0.68	2
5	4	D	357	medium thermal	0.68	2

LS refinement shell

Resolution: 2.25→2.309 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.275	159	-
R_work	0.221	2705	-
obs	-	-	98.39 %

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	0.6503	-0.2828	0.6667	1.1025	0.7807	7.0596	0.0573	0.0689	-0.1076	-0.1418	-0.0297	0.0224	0.2008	0.0081	-0.0275	-0.0721	-0.0152	0.0012	-0.0506	-0.0112	-0.0198	66.2256	39.8585	9.1012
2	0.714	-0.0467	0.0375	2.266	-0.7526	2.1978	-0.0409	-0.0576	0.0225	0.1648	0.0322	-0.0519	-0.0552	-0.0506	0.0087	-0.0512	0.0237	0.0081	-0.0389	-0.0116	-0.0254	62.8203	45.2016	22.18
3	0.8974	0.4888	-0.3753	2.0598	-0.6055	2.6265	0.0229	0.1157	-0.0038	-0.0917	-0.0494	-0.0087	-0.0279	0.027	0.0264	-0.1267	0.0285	-0.0076	-0.031	0.0116	-0.0267	65.43	47.4674	8.7446
4	0.8443	-0.5468	-0.3524	0.8672	0.0833	7.0929	-0.0588	0.017	0.1221	-0.029	0.0044	-0.0242	-0.2623	-0.2252	0.0544	-0.0425	-0.0166	0.0186	-0.0462	-0.0068	-0.0046	69.3192	35.2425	-18.1919
5	1.9964	-0.4861	0.28	1.0468	0.0562	2.362	-0.0683	0.1796	-0.0799	-0.0705	0.0219	-0.07	-0.0074	0.1654	0.0464	0.0154	-0.0064	0.0378	-0.0099	0.0068	-0.0202	74.9726	27.1232	-32.5697
6	1.0575	-0.3188	0.3843	0.8778	-0.3207	2.8413	-0.0157	0.0832	-0.0118	-0.0414	0.013	0.0478	-0.0708	0.0003	0.0027	-0.038	-0.0015	0.0109	-0.0481	-0.0058	-0.007	67.0017	28.8189	-19.4437
7	0.7649	0.3748	0.207	1.1349	-0.1765	7.5821	-0.0309	-0.0015	-0.1279	-0.0166	-0.0355	-0.0584	-0.0958	0.0062	0.0665	-0.0656	-0.0166	-0.0299	0.0258	0.0097	0.0418	34.4389	42.6958	17.792
8	2.9376	0.775	-0.2285	0.9456	0.1843	0.6541	0.0968	-0.4181	-0.1667	0.1728	-0.0935	-0.161	-0.0137	0.0512	-0.0033	-0.0016	-0.0216	-0.0541	0.0967	0.0345	0.0057	36.7656	44.7294	34.414
9	3.701	0.8006	-0.6117	0.4139	-0.1497	0.7885	0.0045	0.0872	0.0769	0.0128	0.0332	-0.0772	-0.0434	-0.0753	-0.0377	-0.041	-0.0043	-0.009	-0.0441	0.0208	0.018	32.4015	47.9765	19.904
10	0.8327	0.0982	-0.669	0.7698	-0.8385	14.3799	0.041	-0.0071	-0.0992	-0.037	0.0207	-0.1048	0.52	-0.39	-0.0617	0.0252	-0.0251	-0.0168	0.0565	-0.0018	0.0804	33.2001	38.5611	-6.1171
11	2.0534	0.4694	-0.3016	1.9955	0.2736	4.1779	-0.0705	0.1789	-0.1222	-0.0633	0.1482	-0.1356	0.0343	-0.0532	-0.0778	0.0282	-0.038	-0.0247	0.0969	-0.0158	0.0466	32.5117	40.1129	-23.1575
12	2.3882	0.6678	0.645	2.458	-0.1875	6.4029	0.1334	-0.0352	-0.1383	-0.0466	0.0915	-0.0229	0.2345	-0.4408	-0.2248	-0.0216	-0.0293	-0.0192	0.066	-0.0013	0.05	27.7046	39.7486	-11.447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	39 - 82	19 - 62
2	X-RAY DIFFRACTION	2	A	A	83 - 156	63 - 136
3	X-RAY DIFFRACTION	3	A	A	157 - 214	137 - 194
4	X-RAY DIFFRACTION	4	B	B	37 - 82	17 - 62
5	X-RAY DIFFRACTION	5	B	B	83 - 143	63 - 123
6	X-RAY DIFFRACTION	6	B	B	144 - 214	124 - 194
7	X-RAY DIFFRACTION	7	C	C	38 - 81	18 - 61
8	X-RAY DIFFRACTION	8	C	C	82 - 143	62 - 123
9	X-RAY DIFFRACTION	9	C	C	144 - 214	124 - 194
10	X-RAY DIFFRACTION	10	D	D	39 - 80	19 - 60
11	X-RAY DIFFRACTION	11	D	D	81 - 144	61 - 124
12	X-RAY DIFFRACTION	12	D	D	145 - 214	125 - 194

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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