PDB-5umf: Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisse...

ID or keywords:

Entry

Database: PDB / ID: 5umf

Title

Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate

Components

Ribulose-phosphate 3-epimerase

Phosphopentose epimerase

Keywords

ISOMERASE / SSGCID /

Ribulose-phosphate 3-epimerase /

metal binding / pentose-phosphate shunt /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose catabolic process / pentose-phosphate shunt /

metal ion binding
Similarity search - Function

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate
Authors: Dranow, D.M. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jan 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5umf.cif.gz	293.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5umf.ent.gz	237.8 KB	Display	PDB format
PDBx/mmJSON format	5umf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3inpS S: Starting model for refinement
Similar structure data	3inp-2 4734 5opq-1 1tqj-d 2fli-2 1r37-1 5opq-2 4av7-1 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
Other databases	TargetTrack: SSGCID-NegoA.18161.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Ribulose-phosphate 3-epimerase

B: Ribulose-phosphate 3-epimerase

C: Ribulose-phosphate 3-epimerase

hetero molecules

77.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribulose-phosphate 3-epimerase

B: Ribulose-phosphate 3-epimerase

C: Ribulose-phosphate 3-epimerase

hetero molecules

A: Ribulose-phosphate 3-epimerase

B: Ribulose-phosphate 3-epimerase

C: Ribulose-phosphate 3-epimerase

hetero molecules

defined by author&software
154 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.730, 70.900, 83.500
Angle α, β, γ (deg.)	90.000, 109.310, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-470- HOH
2	1	A-533- HOH

#1: Protein	Ribulose-phosphate 3-epimerase / Phosphopentose epimerase Mass: 25421.334 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria) Strain: NCCP11945 / Gene: NGK_1119 / Plasmid: NegoA.18161.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4RLV9, ribulose-phosphate 3-epimerase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.25 Å³/Da / Density % sol: 45.28 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: NegoA.18161.a.B1.PS38017 at 26.22 mg/ml mixed 1:1 with an equal volume Morpheus (b3): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium fluoride, sodium ...Details: NegoA.18161.a.B1.PS38017 at 26.22 mg/ml mixed 1:1 with an equal volume Morpheus (b3): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium fluoride, sodium bromide, sodium iodide

Crystal

Density Matthews: 2.25 Å³/Da / Density % sol: 45.28 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.18161.a.B1.PS38017 at 26.22 mg/ml mixed 1:1 with an equal volume Morpheus (b3): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium fluoride, sodium ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2016 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.4→40.684 Å / Num. obs: 132656 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.749 % / B_iso Wilson estimate: 12.94 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.07 / R_rim(I) all: 0.082 / Χ²: 0.969 / Net I/σ(I): 11.09 / Num. measured all: 497286 / Scaling rejects: 20

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique all	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.4-1.44	3.698	0.538	2.34	36256	9818	16492	9804	0.798	0.631	99.9
1.44-1.48	3.706	0.426	2.97	35482	9585		9575	0.851	0.499	99.9
1.48-1.52	3.72	0.331	3.75	34315	9244		9224	0.905	0.387	99.8
1.52-1.57	3.726	0.263	4.66	33544	9014		9002	0.939	0.307	99.9
1.57-1.62	3.741	0.208	5.77	32744	8772		8752	0.957	0.243	99.8
1.62-1.67	3.752	0.176	6.69	31460	8391		8385	0.971	0.206	99.9
1.67-1.74	3.762	0.144	7.96	30834	8216		8196	0.979	0.168	99.8
1.74-1.81	3.767	0.119	9.48	29496	7835		7830	0.985	0.139	99.9
1.81-1.89	3.774	0.1	11.29	28449	7546		7539	0.987	0.117	99.9
1.89-1.98	3.772	0.081	13.38	27164	7227		7201	0.992	0.095	99.6
1.98-2.09	3.772	0.073	15.21	25861	6866		6856	0.992	0.085	99.9
2.09-2.21	3.784	0.065	16.95	24610	6513		6504	0.993	0.075	99.9
2.21-2.37	3.772	0.06	18.27	22962	6102		6088	0.993	0.07	99.8
2.37-2.56	3.785	0.057	19.2	21427	5672		5661	0.994	0.067	99.8
2.56-2.8	3.779	0.055	20.16	19867	5269		5257	0.995	0.064	99.8
2.8-3.13	3.782	0.054	21.36	17868	4733		4725	0.993	0.063	99.8
3.13-3.61	3.772	0.053	22.45	15814	4207		4192	0.995	0.062	99.6
3.61-4.43	3.757	0.053	23.11	13427	3584		3574	0.994	0.062	99.7
4.43-6.26	3.722	0.055	22.98	10218	2754		2745	0.994	0.065	99.7
6.26-40.684	3.55	0.054	22.66	5488	1572		1546	0.993	0.064	98.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	(dev_2621: ???)	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3INP

3inp

Resolution: 1.4→40.684 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.8

	R_factor	Num. reflection	% reflection
R_free	0.1648	2019	1.52 %
R_work	0.1484	-	-
obs	0.1487	132647	99.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 72.43 Å² / B_iso mean: 18.9641 Å² / B_iso min: 7.5 Å²

Refinement step

Cycle: final / Resolution: 1.4→40.684 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5028	0	48	806	5882
B_iso mean	-	-	41.58	31.34	-
Num. residues	-	-	-	-	670

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5530
X-RAY DIFFRACTION	f_angle_d	0.844	7582
X-RAY DIFFRACTION	f_chiral_restr	0.087	875
X-RAY DIFFRACTION	f_plane_restr	0.006	995
X-RAY DIFFRACTION	f_dihedral_angle_d	18.589	2111

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.4-1.435	0.2483	174	0.2313	9262	9436
1.435-1.4738	0.2302	166	0.2062	9304	9470
1.4738-1.5172	0.2253	164	0.1889	9252	9416
1.5172-1.5662	0.1774	138	0.1686	9315	9453
1.5662-1.6221	0.1869	139	0.1566	9258	9397
1.6221-1.6871	0.162	134	0.1535	9379	9513
1.6871-1.7639	0.1953	133	0.1539	9270	9403
1.7639-1.8569	0.1727	133	0.1506	9359	9492
1.8569-1.9732	0.1673	138	0.1432	9328	9466
1.9732-2.1256	0.1698	133	0.1418	9294	9427
2.1256-2.3394	0.1703	144	0.1433	9331	9475
2.3394-2.6779	0.1638	126	0.1429	9382	9508
2.6779-3.3736	0.1504	142	0.1432	9409	9551
3.3736-40.7008	0.1342	155	0.1352	9485	9640

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	2.4836	-0.5606	-1.343	2.2984	1.5118	3.6354	0.0191	-0.1228	-0.1561	0.0932	-0.0193	0.0453	0.148	0.0181	-0.0396	0.1441	0.0052	-0.0197	0.104	0.0385	0.1466	1.2173	-7.3637	16.2059
2	4.0442	1.2144	-4.0406	0.3987	-1.1558	9.2025	-0.0427	0.1417	-0.1519	-0.0256	-0.0114	-0.1007	0.0737	-0.0621	0.1103	0.1501	0.0135	-0.0338	0.0683	0.0063	0.1702	0.8322	-14.256	6.9067
3	0.5978	0.4121	-0.1666	0.9819	-0.2377	0.7608	0.0048	-0.0215	-0.1218	-0.0315	0.0112	-0.0235	0.1385	-0.0041	-0.0153	0.1193	-0.0001	-0.0046	0.0791	0.0078	0.1033	-2.851	-1.8254	7.6969
4	2.0868	0.3111	0.1459	2.7668	0.8155	1.1843	0.0166	-0.0179	-0.0198	-0.0583	-0.0091	0.1179	-0.0111	-0.101	-0.0047	0.0836	-0.0009	-0.0044	0.092	0.0182	0.0655	-10.1307	8.6972	11.7839
5	6.5154	-0.5707	-0.6014	1.4845	-0.4544	0.9415	0.0462	-0.0804	-0.0266	0.025	-0.0588	-0.0881	0.0402	0.0047	0.0084	0.137	-0.0088	-0.0199	0.1233	0.0058	0.0605	0.4353	9.1733	21.0448
6	4.0508	-0.269	-2.5654	1.7655	0.1173	1.6357	-0.063	-0.2562	-0.0517	0.3745	-0.0084	-0.0033	0.0091	-0.2415	0.0777	0.2366	-0.0056	0.0012	0.2652	0.0234	0.0591	-1.2268	7.9694	31.5938
7	3.7031	-1.2369	-1.2876	2.6259	0.861	2.9169	0.0402	-0.24	-0.2131	0.2648	0.0258	-0.1269	0.145	-0.0339	-0.0429	0.1656	-0.0355	-0.0237	0.1054	0.0472	0.0955	1.704	-0.8812	26.4493
8	2.2525	0.2643	-1.1646	2.9642	2.3818	4.9954	0.022	0.027	-0.1559	0.1445	0.1233	-0.3375	0.1281	0.1431	-0.1438	0.1409	0.0024	-0.0319	0.1275	0.0384	0.1604	5.4781	-8.6235	18.6583
9	3.8079	-1.2706	-0.7542	3.2586	-2.0682	4.727	0.0124	-0.4684	-0.225	0.4956	0.1362	-0.1644	-0.0859	0.0215	-0.0917	0.2369	-0.0108	-0.0868	0.1694	0.0938	0.2006	5.456	-13.8466	25.4987
10	1.5772	0.4797	-1.0912	2.4055	-0.9656	1.3849	-0.0062	-0.1176	0.0753	0.0657	0.0477	-0.1128	-0.0254	0.0733	-0.0614	0.1253	-0.0189	-0.0239	0.1471	-0.0466	0.1639	24.8196	37.8058	16.2513
11	3.4195	-1.7026	4.9487	1.2375	-1.6776	8.9857	0.0474	0.0643	0.1178	-0.0408	-0.0486	-0.0473	-0.1098	0.171	0.0247	0.1082	-0.0393	0.0031	0.133	-0.024	0.1759	30.9992	40.9046	6.9599
12	1.1907	-0.041	0.0409	0.1497	-0.0912	0.4893	-0.0053	-0.0047	0.0529	0.0104	0.0185	-0.064	-0.0603	0.1024	-0.0107	0.0936	-0.0173	-0.0092	0.121	-0.0105	0.1183	22.2023	31.4251	7.9547
13	8.1032	0.681	-0.1963	3.6762	-0.6215	2.5293	-0.0709	0.2314	-0.2287	-0.1554	0.066	-0.0377	0.1723	0.0081	0.0126	0.1054	-0.0084	-0.0036	0.0806	-0.0167	0.0628	17.0259	20.9661	5.8126
14	3.0896	0.3113	-0.7064	2.4491	-0.1538	1.2849	-0.0277	-0.0574	-0.1284	0.0332	0.0369	-0.1038	0.0517	0.0965	-0.0074	0.0858	0.0048	-0.0209	0.0962	-0.0046	0.064	16.3915	19.5395	14.4904
15	2.1496	-1.507	0.6941	7.1675	-1.0002	1.0276	-0.0099	-0.0729	0.1478	-0.0161	-0.0015	-0.0497	-0.0327	0.0282	0.0049	0.1007	0.0011	-0.006	0.1408	-0.0371	0.0603	10.8561	28.8967	21.1129
16	4.157	-3.124	2.1337	3.5516	-2.6717	3.1893	0.0349	-0.4357	-0.0404	0.2506	-0.0491	0.0333	0.2345	-0.0433	0.0604	0.2189	-0.0259	-0.0263	0.2735	-0.0129	0.0901	12.7306	27.7856	31.841
17	1.8967	0.5582	-0.5745	1.5262	-0.2164	1.4561	0.1092	-0.2518	0.2343	0.1429	-0.0354	0.0444	-0.0921	0.0846	-0.0827	0.1244	-0.0156	-0.0265	0.184	-0.0549	0.1315	20.6765	37.8848	23.8792
18	1.8313	0.4523	0.2481	3.9177	0.7269	5.121	0.0682	-0.4465	0.2786	0.4617	-0.0189	-0.0387	-0.0231	0.0659	-0.0187	0.1856	-0.0344	-0.0321	0.2746	-0.1442	0.2128	28.3506	44.6056	25.8496
19	2.4013	-0.5681	1.713	1.7292	-0.8861	4.714	0.0442	0.0926	0.1094	-0.1227	0.0274	-0.0077	0.0345	0.0431	-0.108	0.1131	-0.026	0.0279	0.1406	0.0043	0.1574	26.1169	35.6449	-16.1787
20	0.4232	-0.3407	0.1909	5.058	-4.0924	3.3539	-0.0552	0.0107	0.0523	0.1011	0.0079	-0.1189	-0.09	0.0695	0.0997	0.0956	-0.031	0.002	0.1449	-0.0228	0.1759	31.8676	39.4465	-6.874
21	0.525	0.4399	-0.2177	0.7113	-0.302	0.8683	0.021	-0.0069	0.0279	-0.0346	-0.0083	-0.0799	-0.013	0.1084	-0.0096	0.1005	-0.0102	-0.0015	0.1286	0.0009	0.1155	18.6204	32.1112	-7.9138
22	1.0023	0.483	-0.2294	0.6471	-0.293	1.3184	0.0529	-0.0163	0.0135	0.0208	0.0203	-0.1281	-0.1896	0.1432	-0.0468	0.1325	-0.0264	0.0051	0.1265	-0.0023	0.1494	20.0203	41.52	-7.4103
23	4.0535	1.1746	0.4235	4.8273	0.2414	2.1623	0.0285	-0.1985	0.1569	0.1951	-0.0277	0.1346	-0.1156	-0.1357	-0.0035	0.0942	0.0052	0.0085	0.1077	-0.0061	0.0731	7.6007	37.3571	-5.7761
24	2.8064	0.3976	0.2643	2.6017	0.576	1.4303	0.0151	0.0323	0.1915	-0.0637	-0.0117	0.078	-0.1202	-0.0084	0.002	0.0907	-0.0015	0.0018	0.0836	0.0184	0.0777	6.0802	37.5084	-14.4663
25	3.9363	-4.3673	0.2867	6.0453	-0.9872	0.3931	0.2282	0.2402	-0.2827	-0.427	-0.1293	0.3898	0.1848	-0.0997	-0.0283	0.1525	-0.0192	-0.0268	0.1496	-0.0054	0.1193	4.827	26.9043	-24.1096
26	3.2935	-2.2662	-0.2907	4.227	-0.4135	0.6486	-0.0839	-0.0404	0.0271	0.0954	0.0194	-0.1811	-0.0299	0.1187	0.0412	0.1366	-0.0222	0.0056	0.1391	-0.0106	0.0841	15.2606	28.6958	-19.2761
27	3.8052	-3.3103	2.0079	6.5075	-3.1439	3.8559	-0.061	0.4135	0.045	-0.2379	0.0356	0.0666	-0.1309	-0.1289	0.013	0.2036	-0.0407	0.0059	0.2624	0.018	0.0712	11.8513	29.5808	-31.7001
28	3.3115	-0.4949	0.669	2.2347	-0.0439	2.8318	-0.027	0.2773	0.0517	-0.2118	0.0835	-0.1939	-0.0873	0.0904	-0.0702	0.1394	-0.0488	0.0334	0.1366	0.0086	0.0932	21.1396	31.6741	-26.7309
29	2.6749	0.5064	1.3788	2.4006	0.2997	3.7912	0.0618	0.0863	-0.0988	0.0143	0.0676	-0.2726	0.1304	0.2139	-0.0808	0.132	-0.0119	0.032	0.1468	-0.0084	0.1444	29.3478	32.5581	-18.6069
30	5.356	0.825	0.4046	4.1936	1.7476	6.5022	-0.026	0.6022	0.0151	-0.5225	0.1964	-0.1976	-0.2084	0.1355	-0.1009	0.1766	-0.0425	0.0871	0.206	-0.0128	0.1754	33.5633	35.3148	-26.2021

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 14 )	A	3 - 14
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 27 )	A	15 - 27
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 69 )	A	28 - 69
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 116 )	A	70 - 116
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 117 through 150 )	A	117 - 150
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 151 through 171 )	A	151 - 171
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 194 )	A	172 - 194
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 195 through 210 )	A	195 - 210
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 211 through 225 )	A	211 - 225
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 14 )	B	3 - 14
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 15 through 27 )	B	15 - 27
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 28 through 69 )	B	28 - 69
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 70 through 82 )	B	70 - 82
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 116 )	B	83 - 116
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 117 through 150 )	B	117 - 150
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 151 through 171 )	B	151 - 171
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 172 through 210 )	B	172 - 210
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 211 through 225 )	B	211 - 225
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 3 through 14 )	C	3 - 14
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 15 through 27 )	C	15 - 27
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 28 through 49 )	C	28 - 49
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 50 through 69 )	C	50 - 69
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 70 through 82 )	C	70 - 82
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 83 through 116 )	C	83 - 116
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 117 through 128 )	C	117 - 128
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 129 through 150 )	C	129 - 150
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 151 through 171 )	C	151 - 171
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 172 through 194 )	C	172 - 194
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 195 through 210 )	C	195 - 210
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 211 through 226 )	C	211 - 226

-
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