PDB-13gn: Crystal Structure of L-erythrulose-1-phosphate isomerase from Bru...

ID or keywords:

Entry

Database: PDB / ID: 13gn

Title

Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE

Components

L-erythrulose-1-phosphate isomerase

Keywords

ISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / L-erythrulose-1-phosphate isomerase / Brucella melitensis

Function / homology

Function and homology information

L-erythrulose-1-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function

Biological species

Brucella abortus 2308 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	May 5, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 20, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	13gn.cif.gz	390.7 KB	Display	PDBx/mmCIF format
PDB format	pdb13gn.ent.gz	321 KB	Display	PDB format
PDBx/mmJSON format	13gn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/3g/13gn ftp://data.pdbj.org/pub/pdb/validation_reports/3g/13gn	HTTPS FTP

-
Related structure data

Similar structure data	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	#50 - Feb 2004 Glycolytic Enzymes similarity (6)

Deposited unit

A: L-erythrulose-1-phosphate isomerase

B: L-erythrulose-1-phosphate isomerase

C: L-erythrulose-1-phosphate isomerase

D: L-erythrulose-1-phosphate isomerase

hetero molecules

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

1

A: L-erythrulose-1-phosphate isomerase

D: L-erythrulose-1-phosphate isomerase

hetero molecules

defined by author&software
Evidence: gel filtration, dimeric
57.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: L-erythrulose-1-phosphate isomerase

C: L-erythrulose-1-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.802, 49.525, 104.793
Angle α, β, γ (deg.)	92.72, 96.10, 93.72
Int Tables number	1
Space group name H-M	P1

#1: Protein	L-erythrulose-1-phosphate isomerase / D-3-tetrulose-4-phosphate isomerase Mass: 28744.627 Da / Num. of mol.: 4 / Fragment: K3-N256 / Mutation: A173D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: eryH, tpiA-2, BAB2_0367 / Plasmid: BrabA.00276.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2YIQ6, L-erythrulose-1-phosphate isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₉O₆P / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 39.95 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), 1GP fit best to the electron ...Details: 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), 1GP fit best to the electron density, plate Liu-S-202 E9-F10, Puck: PSL-0208, Cryo: 100 mM MES, pH 6.5, 100 mM CaCl2, 20% PEG 1500, 12% hexanediol

Crystal

Density Matthews: 2.05 Å³/Da / Density % sol: 39.95 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), 1GP fit best to the electron ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 22, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.95→45.56 Å / Num. obs: 64555 / % possible obs: 97 % / Redundancy: 3.6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.07 / R_rim(I) all: 0.133 / Χ²: 1.05 / Net I/σ(I): 9 / Num. measured all: 230370
Reflection shell	Resolution: 1.95→2 Å / % possible obs: 96.6 % / Redundancy: 3.7 % / R_merge(I) obs: 0.888 / Num. measured all: 17637 / Num. unique obs: 4781 / CC_1/2: 0.644 / R_pim(I) all: 0.538 / R_rim(I) all: 1.04 / Χ²: 0.95 / Net I/σ(I) obs: 1.6

-
Processing

Software

Name	Version	Classification
PHENIX	(2.1rc2_6044: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→45.56 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2163	3331	5.16 %
R_work	0.1622	-	-
obs	0.165	64538	96.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→45.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7392	0	18	573	7983

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7586
X-RAY DIFFRACTION	f_angle_d	1.027	10289
X-RAY DIFFRACTION	f_dihedral_angle_d	16.727	2778
X-RAY DIFFRACTION	f_chiral_restr	0.057	1163
X-RAY DIFFRACTION	f_plane_restr	0.012	1338

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-1.98	0.3712	139	0.2723	2626	X-RAY DIFFRACTION	96
1.98-2.01	0.3392	116	0.2555	2459	X-RAY DIFFRACTION	96
2.01-2.04	0.29	148	0.2318	2556	X-RAY DIFFRACTION	97
2.04-2.07	0.2973	131	0.2172	2569	X-RAY DIFFRACTION	97
2.07-2.11	0.2584	141	0.2027	2542	X-RAY DIFFRACTION	96
2.11-2.15	0.2429	136	0.1993	2509	X-RAY DIFFRACTION	96
2.15-2.19	0.2683	149	0.1935	2569	X-RAY DIFFRACTION	97
2.19-2.23	0.2697	148	0.1847	2489	X-RAY DIFFRACTION	97
2.23-2.28	0.233	143	0.1785	2569	X-RAY DIFFRACTION	97
2.28-2.33	0.2441	141	0.1745	2540	X-RAY DIFFRACTION	97
2.33-2.39	0.2724	128	0.1697	2566	X-RAY DIFFRACTION	97
2.39-2.46	0.2472	142	0.1581	2517	X-RAY DIFFRACTION	97
2.46-2.53	0.2225	120	0.1615	2615	X-RAY DIFFRACTION	98
2.53-2.61	0.2237	144	0.1476	2557	X-RAY DIFFRACTION	97
2.61-2.7	0.2503	132	0.1644	2540	X-RAY DIFFRACTION	97
2.7-2.81	0.2256	121	0.1606	2610	X-RAY DIFFRACTION	98
2.81-2.94	0.192	124	0.1642	2564	X-RAY DIFFRACTION	97
2.94-3.1	0.2224	138	0.1643	2598	X-RAY DIFFRACTION	98
3.1-3.29	0.1892	129	0.155	2560	X-RAY DIFFRACTION	97
3.29-3.54	0.1889	141	0.151	2549	X-RAY DIFFRACTION	97
3.54-3.9	0.1973	171	0.1383	2486	X-RAY DIFFRACTION	97
3.9-4.46	0.1594	152	0.1244	2505	X-RAY DIFFRACTION	96
4.46-5.62	0.1834	133	0.1313	2570	X-RAY DIFFRACTION	97
5.62-45.56	0.1998	164	0.1672	2542	X-RAY DIFFRACTION	98

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	1.1689	0.4151	0.6219	6.2196	2.5183	3.9492	-0.0634	0.0672	-0.0566	-0.4579	-0.0717	0.239	-0.1573	-0.1774	0.1357	0.1778	-0.0013	-0.0324	0.214	0.0094	0.1897	17.7869	29.6302	78.5153
2	6.3544	4.0775	5.8016	6.1635	4.5223	6.1585	-0.1066	-0.0425	0.4414	-0.4053	-0.0891	0.8285	-0.1746	-0.548	0.1881	0.2376	0.0217	-0.0774	0.237	0.0268	0.3094	10.6596	40.0623	78.184
3	1.9174	-1.5314	-1.2698	3.3886	-0.435	1.8103	-0.0052	0.341	-0.4923	-0.4863	-0.0269	0.6643	0.1199	-0.2786	0.0428	0.3719	-0.0347	-0.1089	0.2476	-0.0084	0.3339	8.8113	27.1878	75.9073
4	4.4061	-0.297	2.95	1.7016	0.334	4.3079	-0.0176	-0.1747	-0.1309	-0.2087	0.0574	0.3762	-0.1416	-0.358	-0.0195	0.2439	0.017	-0.0363	0.2398	0.0265	0.2564	12.5315	32.553	87.0531
5	1.415	-0.3255	0.9854	1.9915	0.8844	3.2394	-0.017	-0.2262	-0.1126	0.0532	0.0212	0.1193	0.2459	-0.281	-0.0133	0.2211	-0.0277	-0.0183	0.2102	0.0269	0.2448	18.6743	27.9226	95.7477
6	2.5646	0.7766	-1.2686	2.2394	0.1156	2.3683	-0.0992	-0.0653	0.0625	-0.1662	0.0962	-0.2634	0.1875	0.1995	0.0156	0.2445	0.03	-0.0051	0.2082	0.0304	0.2898	27.7384	19.2573	88.2358
7	3.4389	-1.1625	-4.8264	5.3214	1.7388	6.7762	-0.201	-0.2944	-0.6912	-0.5872	0.0621	-0.0351	0.2385	0.3808	0.1	0.2987	0.0152	-0.0041	0.2346	0.0227	0.2828	28.9136	9.6536	86.2082
8	1.6045	-0.1236	-1.5687	1.9044	-0.1174	4.2659	-0.0751	0.0413	-0.0814	-0.378	0.0026	0.0645	0.0959	0.0458	0.0623	0.3332	0.0047	-0.06	0.1742	0.0057	0.2803	20.9719	13.9652	85.0967
9	0.1902	0.3832	-0.2805	3.7347	-2.6026	2.4988	0.002	0.0669	-0.0458	-0.6933	-0.0013	0.0535	0.2209	-0.0479	0.0165	0.3917	0.0114	-0.0262	0.1948	-0.0128	0.2574	21.9987	12.3768	76.2747
10	1.8598	1.8858	0.1322	4.5859	0.4703	2.1686	-0.1878	0.2457	-0.0324	-0.4292	0.3167	0.1028	0.2114	-0.0122	-0.102	0.47	-0.0106	-0.071	0.2168	-0.0088	0.2169	19.9064	22.2733	70.5731
11	6.7757	-2.3384	-1.1006	5.4541	1.7542	8.3567	0.0616	0.3997	-0.1842	-0.3101	-0.2796	0.1994	0.6497	-0.5684	0.2718	0.4627	-0.0152	-0.1042	0.2847	-0.0192	0.3169	12.9523	26.8567	66.4702
12	2.7683	0.7409	-0.1578	3.7548	2.3365	5.5427	-0.0619	0.2155	-0.0812	-0.0424	-0.0666	0.2849	0.3452	-0.0995	0.1155	0.1983	-0.0034	-0.0153	0.1966	0.0123	0.2015	16.3617	24.4057	35.9746
13	5.6701	2.8752	-0.1195	8.1768	4.0366	6.675	-0.047	-0.2131	-0.1072	0.8805	-0.009	0.2386	0.6014	-0.456	0.0456	0.3017	-0.0197	0.0016	0.2293	0.0012	0.2548	11.4696	20.9895	47.0217
14	3.3098	-0.1374	0.8315	1.8459	-0.3032	5.1586	0.0597	-0.1387	-0.15	0.1871	-0.0135	0.0847	0.1333	-0.1786	-0.0253	0.1714	-0.0037	0.0282	0.1898	-0.011	0.2014	19.1241	19.6284	41.6041
15	2.7164	1.2177	-0.9872	2.0326	-0.395	1.6024	0.0016	0.0981	-0.1772	-0.0974	0.084	-0.2416	0.1007	0.0563	-0.0676	0.2359	0.0135	-0.0201	0.1904	-0.007	0.2178	30.4585	26.4528	40.8121
16	1.627	-0.6024	0.2913	2.0567	-0.5255	3.0493	-0.0179	0.1596	0.0213	0.0623	-0.0406	-0.0163	-0.0536	-0.0181	0.0489	0.2173	-0.0247	-0.0037	0.2129	-0.0143	0.2116	30.9125	28.6906	34.6108
17	3.5686	-0.9393	0.1694	3.5252	-1.0434	4.361	-0.0172	0.5723	0.3885	-0.4827	-0.0577	0.2499	-0.2046	-0.0709	0.121	0.3093	-0.0192	-0.0623	0.3035	0.0185	0.2967	25.1583	31.8898	22.1026
18	5.8526	-3.8799	4.8268	3.8666	-3.3523	8.6517	-0.008	0.4815	0.2232	-0.355	-0.2247	-0.2653	-0.4025	0.2299	0.2223	0.3524	-0.0105	-0.001	0.4047	0.0021	0.2226	31.2401	29.3588	17.9521
19	5.6126	-0.799	1.817	2.7857	-0.3692	3.5056	0.0168	0.3364	0.0303	-0.218	0.0515	-0.0762	0.2705	0.226	-0.0692	0.3188	-0.004	0.0111	0.2575	-0.0453	0.2138	29.9855	22.2156	24.2919
20	6.1407	-1.1935	-0.5668	2.3254	0.322	3.1854	0.1865	0.3235	-0.1162	-0.4139	-0.0986	0.2202	0.1828	0.0063	-0.0784	0.2997	-0.0087	-0.044	0.2521	-0.0023	0.2053	20.9881	22.3053	18.8921
21	3.8403	-0.7881	-0.9879	3.2807	1.6183	8.0206	-0.2346	0.2689	0.0135	-0.4439	0.0689	0.3725	-0.1162	-0.3971	0.1624	0.3055	-0.0511	-0.0735	0.2135	0.0249	0.2707	12.076	22.7438	25.9603
22	5.3886	0.7424	1.6469	5.1994	0.5478	8.4143	-0.2059	0.3935	-0.1834	-0.1918	0.3816	0.1139	0.1559	-0.3232	-0.1376	0.2351	-0.06	-0.0083	0.2633	0.0207	0.3681	6.3782	17.455	31.0996
23	2.0243	1.0164	0.7703	7.1467	2.5621	3.3327	0.0115	-0.0422	-0.003	0.66	0.0928	-0.2577	0.2156	0.3059	-0.0686	0.2494	0.0016	-0.034	0.2208	0.0232	0.1993	36.6205	38.9749	55.8921
24	1.112	-0.226	-1.0639	4.7725	4.7168	6.5317	0.0724	-0.0622	-0.1117	0.5473	-0.0378	0.001	0.9266	0.0778	-0.0004	0.4042	0.0206	-0.0638	0.2223	0.0193	0.2341	34.8734	29.3812	63.546
25	0.9106	0.0475	0.3563	1.4464	-0.485	2.507	0.0142	-0.0961	0.034	0.2089	-0.0249	0.0424	-0.0722	-0.081	0.0348	0.2613	0.011	-0.0152	0.1568	-0.0101	0.1875	26.0988	38.4489	53.5859
26	2.5245	-1.1558	-1.8146	2.5871	0.675	3.4989	0.0822	0.1074	0.0341	-0.2623	-0.0881	0.0718	-0.3405	-0.0204	-0.0225	0.3021	-0.0117	-0.0318	0.1981	-0.0083	0.2333	28.2053	47.3026	41.8371
27	9.4977	4.3129	-3.9479	3.6539	-1.6736	2.4877	-0.0509	0.4393	0.1827	0.094	0.1934	-0.0732	-0.0411	-0.0361	-0.1903	0.2909	-0.0124	-0.0411	0.2149	-0.0119	0.2494	36.9614	53.3152	44.6283
28	4.0597	1.0918	-0.6778	0.7705	-0.4802	1.4636	0.1773	-0.081	0.2237	0.1672	-0.0367	-0.0324	0.0144	0.133	-0.131	0.4031	0.0014	-0.0258	0.1726	-0.0316	0.2497	31.8627	56.0707	48.364
29	2.8381	-0.5705	-0.4458	3.0112	-0.6517	1.6103	0.1378	-0.1584	0.2122	0.1835	-0.1521	-0.2588	-0.3718	0.283	0.0229	0.3538	-0.0534	-0.0825	0.2157	-0.0092	0.2629	39.1266	56.6001	54.2726
30	2.6295	1.2306	0.9744	1.8227	1.521	3.3501	-0.1851	0.2607	-0.0051	0.1263	0.2588	-0.4292	-0.3352	0.668	-0.0864	0.3197	-0.0656	-0.0815	0.3408	0.0147	0.2763	43.9895	46.9034	58.1352
31	9.1922	4.5572	1.9337	7.3997	3.6461	9.1808	-0.1482	-0.2508	-0.0217	0.8609	0.2697	-0.7818	-0.0064	0.381	-0.1026	0.3978	0.0023	-0.1556	0.3059	0.0081	0.286	44.702	41.4539	65.7801
32	2.8176	0.0644	-0.2199	1.5558	0.0317	2.2335	0.0056	-0.197	0.1975	0.1778	-0.032	0.0707	-0.1985	-0.0702	0.0424	0.1594	0.0283	0.014	0.2036	-0.0173	0.1932	19.5878	47.185	106.8842
33	1.3711	-0.802	-0.7459	2.2395	0.9476	2.9255	-0.1069	0.0837	0.0886	-0.0021	0.0496	0.1491	-0.2746	-0.1298	0.0866	0.1934	0.0096	-0.03	0.203	0.0308	0.2775	20.4485	46.0149	97.3542
34	1.4618	0.5159	0.796	1.3953	-0.0163	1.2739	0.0144	0.008	-0.0809	-0.1355	0.0089	-0.1465	0.0811	0.0759	-0.0106	0.1874	0.0219	0.0225	0.2168	-0.0136	0.2237	32.0639	39.691	92.0575
35	2.9221	-1.1542	0.6657	5.0295	-2.4633	2.8856	-0.1225	-0.1362	-0.01	0.5524	-0.1508	-0.4688	-0.1196	0.2631	0.2469	0.1838	-0.0183	-0.026	0.271	0.01	0.2616	40.5952	38.2232	105.4025
36	2.878	-2.156	2.8532	4.4401	-3.6093	8.8315	0.0226	-0.2392	0.0781	0.2205	-0.2305	-0.5313	0.0601	0.3469	0.164	0.1668	-0.0248	0.0005	0.388	0.0197	0.3996	47.6868	40.0758	102.7542
37	3.0949	0.2263	-0.8165	5.928	-2.2487	5.7204	0.0791	-0.0431	0.1368	0.1494	-0.2276	-0.3643	-0.2608	0.4104	0.1255	0.0814	-0.0391	-0.0171	0.2019	-0.0014	0.2755	40.673	47.5858	99.7647
38	4.6114	-0.045	-1.0652	3.3564	-2.0194	8.1956	0.0812	-0.4217	0.2594	0.3877	0.0103	-0.5235	-0.2416	0.5093	-0.0666	0.2633	-0.049	-0.0848	0.2982	-0.071	0.3778	45.5081	46.4079	110.3637
39	6.0863	2.5182	-4.7212	2.9756	-3.1771	6.9818	0.2574	-0.5738	0.3686	0.4699	-0.039	0.1258	-0.4735	0.102	-0.1695	0.2405	0.0243	-0.0631	0.2778	-0.039	0.29	35.34	46.7119	112.1274
40	7.5183	3.6063	0.9548	3.8311	0.4541	2.846	0.1862	-0.6831	0.0403	0.3715	-0.0603	-0.1005	-0.0623	-0.0363	-0.1389	0.276	0.0145	-0.0405	0.2718	-0.0222	0.2172	30.8223	45.4776	115.6429
41	7.1318	0.3525	2.728	6.7977	1.1279	2.0393	0.0604	-1.0613	0.3607	0.6608	-0.1894	0.2721	-0.5881	-0.5269	0.0775	0.3937	0.0071	0.0851	0.3736	-0.0257	0.2136	23.1432	50.3726	118.2367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 44 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 45 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 96 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 97 through 139 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 140 through 152 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 153 through 183 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 184 through 217 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 218 through 238 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 239 through 253 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 15 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 16 through 29 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 30 through 54 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 55 through 80 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 81 through 119 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 120 through 139 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 140 through 152 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 153 through 182 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 183 through 217 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 218 through 238 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 239 through 253 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 3 through 15 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 16 through 32 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 33 through 96 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 97 through 119 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 120 through 139 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 140 through 182 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 183 through 217 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 218 through 238 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 239 through 253 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 3 through 44 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 45 through 68 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 69 through 119 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 120 through 139 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 140 through 151 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 152 through 182 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 183 through 201 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 202 through 217 )
40	X-RAY DIFFRACTION	40	chain 'D' and (resid 218 through 238 )
41	X-RAY DIFFRACTION	41	chain 'D' and (resid 239 through 254 )

-
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