PDB-5bt8: X-ray Crystal Structure of phosphoglycerate kinase from Acinetoba...

ID or keywords:

Entry

Database: PDB / ID: 5bt8

Title

X-ray Crystal Structure of phosphoglycerate kinase from Acinetobacter baumannii

Components

Phosphoglycerate kinase

Keywords

TRANSFERASE / phosphoglycerate kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / ATP binding / cytosol
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: X-ray Crystal Structure of phosphoglycerate kinase from Acinetobacter baumannii
Authors: Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Author supporting evidence / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 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	5bt8.cif.gz	839.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5bt8.ent.gz	698.6 KB	Display	PDB format
PDBx/mmJSON format	5bt8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5bt8_validation.pdf.gz	460.6 KB	Display	wwPDB validaton report
Full document	5bt8_full_validation.pdf.gz	471.4 KB	Display
Data in XML	5bt8_validation.xml.gz	77.5 KB	Display
Data in CIF	5bt8_validation.cif.gz	108.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/5bt8 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5bt8	HTTPS FTP

-
Related structure data

Related structure data	1zmrS S: Starting model for refinement
Similar structure data	4fey-d 6i06-d 3zlb-d 1eps-d 2xci-4 6hxe-d 4fkc-d 4ehj-1 2xci-5 5oea-1 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
Other databases	TargetTrack: SSGCID-AcbaC.01331.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (7)

Deposited unit

A: Phosphoglycerate kinase

B: Phosphoglycerate kinase

C: Phosphoglycerate kinase

D: Phosphoglycerate kinase

E: Phosphoglycerate kinase

F: Phosphoglycerate kinase

254 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Phosphoglycerate kinase

defined by software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.440, 200.290, 87.300
Angle α, β, γ (deg.)	90.000, 91.370, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IN UNKNOWN

#1: Protein	Phosphoglycerate kinase Mass: 42341.211 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB5075 / Gene: pgk, A591_A2233 / Plasmid: AcbaC.01331.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A0A2T205, UniProt: A0A0M3KL68*PLUS, phosphoglycerate kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Phosphoglycerate kinase

Mass: 42341.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter baumannii (bacteria) / Strain: AB5075 / Gene: pgk, A591_A2233 / Plasmid: AcbaC.01331.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0A2T205, UniProt: A0A0M3KL68*PLUS, phosphoglycerate kinase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.47 Å³/Da / Density % sol: 50.15 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: MCSG1 screen H9: 0.1 M BIS-TRIS:HCl, pH 5.6, 25% PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 106790 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.82 % / B_iso Wilson estimate: 33.21 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.085 / Χ²: 0.992 / Net I/σ(I): 14.03 / Num. measured all: 408424

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.3-2.36		0.853	0.546	2.61	30643	7952	7936	0.635	99.8
2.36-2.42		0.909	0.406	3.38	29776	7697	7695	0.472	100
2.42-2.49		0.928	0.342	3.99	28740	7430	7427	0.397	100
2.49-2.57		0.943	0.289	4.73	28116	7265	7262	0.335	100
2.57-2.66		0.959	0.228	5.97	27227	7036	7034	0.264	100
2.66-2.75		0.969	0.191	7.01	26391	6819	6816	0.221	100
2.75-2.85		0.978	0.149	8.86	25276	6546	6545	0.173	100
2.85-2.97		0.985	0.12	10.79	24438	6343	6341	0.139	100
2.97-3.1		0.989	0.097	13.06	23448	6099	6098	0.113	100
3.1-3.25		0.993	0.076	16.2	22153	5797	5791	0.089	99.9
3.25-3.43		0.995	0.066	18.47	20950	5503	5500	0.077	99.9
3.43-3.64		0.995	0.058	21	19920	5266	5258	0.067	99.8
3.64-3.89		0.995	0.052	23.71	18458	4906	4900	0.061	99.9
3.89-4.2		0.997	0.044	26.69	17162	4579	4574	0.051	99.9
4.2-4.6		0.998	0.038	29.48	15698	4202	4193	0.044	99.8
4.6-5.14		0.998	0.037	30.13	14313	3825	3819	0.043	99.8
5.14-5.94		0.998	0.036	29.46	12714	3362	3355	0.042	99.8
5.94-7.27		0.998	0.033	31.21	10748	2858	2853	0.039	99.8
7.27-10.29		0.998	0.028	35.45	8136	2209	2202	0.033	99.7
	10.29	0.998	0.027	36.08	4117	1243	1191	0.032	95.8

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	(dev_2050)	refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZMR

1zmr

Resolution: 2.3→48.45 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2481	2003	1.88 %	RANDOM
R_work	0.2151	104727	-	-
obs	0.2157	106730	99.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 98.19 Å² / B_iso mean: 40.8111 Å² / B_iso min: 14.14 Å²

Refinement step

Cycle: final / Resolution: 2.3→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17028	0	0	410	17438
B_iso mean	-	-	-	35.52	-
Num. residues	-	-	-	-	2376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	17304
X-RAY DIFFRACTION	f_angle_d	0.783	23616
X-RAY DIFFRACTION	f_chiral_restr	0.038	2886
X-RAY DIFFRACTION	f_plane_restr	0.003	3107
X-RAY DIFFRACTION	f_dihedral_angle_d	14.016	10354

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.3575	0.329	141	0.2834	7494	7635	100
2.3575-2.4213	0.3523	148	0.2742	7475	7623	100
2.4213-2.4925	0.356	138	0.2758	7401	7539	100
2.4925-2.573	0.3519	148	0.267	7480	7628	100
2.573-2.6649	0.3436	147	0.2602	7465	7612	100
2.6649-2.7716	0.294	136	0.262	7484	7620	100
2.7716-2.8977	0.2759	145	0.2538	7449	7594	100
2.8977-3.0505	0.3208	135	0.2637	7515	7650	100
3.0505-3.2416	0.2808	144	0.2574	7487	7631	100
3.2416-3.4918	0.3068	135	0.239	7509	7644	100
3.4918-3.8431	0.2219	147	0.2073	7462	7609	100
3.8431-4.3988	0.194	146	0.1781	7499	7645	100
4.3988-5.5408	0.1837	152	0.1571	7477	7629	100
5.5408-48.4607	0.1515	141	0.1509	7530	7671	99

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	2.1905	-0.7221	0.2396	3.3479	-0.1195	2.6602	0.1252	-0.0994	-0.1011	0.002	-0.2036	0.3791	0.3319	-0.2198	0.0549	0.3211	-0.0497	0.0154	0.2407	-0.024	0.2359	-1.6312	-12.6853	36.8266
2	1.7509	1.9788	-0.148	4.862	0.2238	0.3407	0.1373	-0.2093	0.0085	-0.0548	-0.0905	-0.5434	-0.0442	0.0769	-0.0564	0.2984	0.0242	0.0064	0.3126	-0.0539	0.3328	24.6572	5.0835	38.4338
3	0.579	1.0923	-0.3123	4.4028	-0.5268	2.0256	0.1225	0.1431	0.5343	-0.5451	0.0409	-0.0531	-0.0865	-0.0207	-0.1131	0.6521	0.0216	0.0641	0.3504	-0.0285	0.5344	20.4767	30.0224	28.4772
4	0.6315	0.2134	0.0498	2.5879	0.3305	0.3251	-0.0112	0.1122	-0.0277	-0.8593	0.0278	-0.3361	-0.0352	0.0253	0.0484	0.5524	0.0167	0.122	0.3128	-0.0555	0.3306	22.4181	5.3207	28.0641
5	3.3851	-0.1574	0.223	1.7989	-0.8317	2.2872	-0.321	-0.1845	-0.3261	-0.1148	0.2156	0.1694	0.3355	0.1767	0.111	0.342	0.0222	0.06	0.2579	-0.0095	0.2136	-7.5821	-46.2776	57.1259
6	3.6528	0.6215	-0.0011	3.214	0.721	3.2414	-0.1154	0.0525	-0.13	-0.1798	0.0858	-0.2197	0.1161	0.4384	0.0583	0.3277	0.0314	0.0477	0.2631	-0.0005	0.1874	-0.342	-46.0961	48.9146
7	3.3504	-2.497	-1.2056	5.0736	0.8486	1.1084	0.1475	0.3043	-0.061	-0.3402	-0.3532	0.5891	-0.1154	-0.1626	0.0792	0.3691	-0.0897	-0.0732	0.2811	-0.0241	0.2843	-20.8132	-40.0127	47.7051
8	1.6891	0.5463	0.2468	5.1345	0.3355	1.944	-0.0065	0.1835	-0.0767	-0.2029	0.0974	0.6912	0.0252	-0.0912	-0.0542	0.1898	-0.0099	-0.033	0.2907	0.0206	0.3488	-25.5292	-9.4123	51.4067
9	0.2327	-0.081	0.1979	5.0774	0.2681	0.124	-0.0265	0.0464	-0.0458	0.4073	0.1292	0.5372	0.0748	-0.0467	-0.1072	0.3096	-0.0196	0.0672	0.3053	-0.0047	0.353	-24.6354	-23.222	58.0203
10	3.115	1.4605	0.5792	2.6461	-0.6427	2.479	-0.1981	0.2957	-0.221	-0.239	0.1313	-0.038	0.2465	0.1091	0.0132	0.2709	-0.0269	0.0828	0.3075	-0.0238	0.2935	34.3964	6.4592	-10.1158
11	2.2624	1.5275	0.443	2.8477	0.4298	0.0678	-0.093	-0.0181	0.4511	-0.2863	-0.0271	0.2967	-0.0633	-0.0283	0.1251	0.2405	0.0014	-0.0051	0.2755	-0.0338	0.2663	26.3898	7.1186	-4.6432
12	2.5824	-0.7089	0.5232	6.475	0.2701	2.0005	0.0926	-0.2829	-0.2092	-0.0543	-0.2119	0.5997	0.4221	-0.175	0.0974	0.2786	0.012	0.0163	0.281	-0.0324	0.3012	6.1007	-24.931	-6.5561
13	1.6148	0.9521	0.0478	2.492	-0.0424	1.0813	-0.0391	0.0454	0.2269	-0.8464	-0.2062	0.4554	-0.1349	0.0025	0.2413	0.3724	0.0639	-0.1068	0.3144	0.0095	0.3586	11.1437	-8.495	-14.4614
14	2.0613	1.0117	0.5808	1.926	0.1082	1.1779	0.1166	-0.2703	0.1675	-0.0311	-0.2236	0.105	-0.1417	-0.0603	0.1007	0.2027	0.0187	0.1047	0.2794	-0.0345	0.2727	-34.4097	-23.5959	16.6172
15	2.145	-0.1309	0.5259	3.438	-0.6734	1.7915	0.1103	-0.0697	-0.0328	-0.2026	-0.2121	0.6815	-0.0252	-0.1859	0.1046	0.2102	0.0258	0.0405	0.2619	-0.0826	0.3952	-39.7153	-23.9892	7.7308
16	1.22	-1.2468	0.2226	1.4245	-0.0604	0.1672	0.2559	0.1575	0.3726	-0.6436	-0.4083	-0.8322	-0.0124	0.1994	0.0115	0.3672	0.0942	0.15	0.3018	0.061	0.4998	-13.5394	-34.5136	6.4799
17	1.0978	0.1987	0.4531	1.6168	-1.0082	0.9372	0.3162	0.7251	-0.1597	-1.2193	-0.4585	-0.8545	0.5855	0.593	0.4376	0.7132	0.4312	0.3999	0.5838	0.1324	0.5723	-7.104	-52.3538	2.7834
18	1.1012	0.3685	-0.7141	1.6263	-0.1291	4.3809	0.2857	0.5198	-0.5895	-0.559	-0.3721	-0.2043	0.7966	-0.0409	0.0543	0.4786	0.0964	0.0032	0.3567	0.0177	0.5228	-14.7967	-65.3649	14.6943
19	2.0059	-1.2542	0.5455	0.7877	-0.3725	1.4082	0.0923	-0.3453	0.5026	0.3684	-0.2755	-1.0068	-0.2115	0.4576	0.081	0.2223	0.0835	-0.0457	0.386	0.078	0.6089	-8.862	-48.5217	17.7431
20	1.5452	-1.2538	0.4926	5.8211	-1.9413	0.8294	0.1071	0.0397	-0.0253	0.0768	-0.3134	-0.5392	-0.1525	0.2694	0.1153	0.2283	0.0196	0.0854	0.309	0.0462	0.3404	-17.2177	-34.0215	11.8695
21	1.5361	0.4213	-0.0675	2.0294	0.4278	1.9922	0.0344	0.0174	0.098	0.0786	-0.0219	-0.3628	-0.0477	0.1906	0.0087	0.189	0.0203	-0.042	0.2101	-0.0209	0.3477	2.4931	22.0387	52.79
22	2.8254	-1.4172	-0.0707	2.5172	0.1002	0.9916	0.0523	0.3755	-0.0503	-0.4435	-0.1837	0.5369	-0.1874	-0.1913	0.1104	0.321	0.0186	-0.0526	0.2637	-0.0587	0.3424	-16.3135	23.1135	46.4552
23	2.1885	-0.0614	0.4172	1.3418	1.0866	1.8618	0.145	0.3907	-0.0712	-1.0062	-0.1929	0.5869	-0.504	-0.1457	0.0559	0.5037	0.1456	-0.1976	0.3762	-0.0461	0.4973	-28.285	47.8717	42.568
24	3.304	0.1286	-1.2496	2.0502	0.8913	3.3081	0.0995	-0.0722	0.8433	-0.1133	0.003	-0.1272	-0.9263	-0.0744	-0.2533	0.3973	0.0459	0.0347	0.3251	0.0241	0.5211	-20.5738	62.4835	55.8991
25	0.8467	-0.7088	-0.09	2.2403	0.8204	0.928	0.1126	-0.0083	-0.0048	-0.1206	-0.2515	0.4469	-0.1687	-0.1628	0.1071	0.2126	0.0172	-0.0324	0.3329	-0.019	0.4773	-24.2064	40.5027	54.3391
26	0.7458	0.2805	-0.0566	1.87	-0.4559	1.8555	-0.4203	-0.0806	0.5292	0.0974	0.3064	0.122	-0.2906	-0.2518	0.0576	0.4483	0.0198	-0.2072	0.2967	0.0549	0.5646	-29.7397	43.9734	96.5944
27	3.7726	0.0632	1.6595	1.5444	0.5622	6.639	-0.2876	-0.2084	0.25	-0.1952	0.1328	0.7672	-0.1091	-0.6364	0.2994	0.4485	-0.0441	-0.1003	0.3849	0.0104	0.6035	-40.3262	40.2067	94.0225
28	1.3516	0.3049	1.7552	0.2942	0.1721	2.4955	-0.3434	-0.1204	0.8499	-0.2803	-0.1307	0.6003	-0.397	-0.5963	0.5092	0.6321	-0.082	-0.3861	0.5355	0.0576	0.8569	-37.8387	48.1307	88.7205
29	0.7999	0.5788	0.1888	2.4898	-0.6451	1.3853	-0.4508	0.4895	0.4072	-0.3869	0.2204	-0.0669	-0.2476	0.0902	0.154	0.4829	-0.1704	-0.1073	0.4073	0.113	0.4296	-22.455	39.8086	85.0061
30	2.1505	0.0537	0.7863	4.8957	-1.5562	3.2394	0.1085	0.408	-0.0634	-0.4025	-0.0556	-0.0922	0.0313	0.4181	-0.0076	0.2263	-0.0161	0.0563	0.3658	-0.0615	0.3762	-11.3011	10.1027	89.1548
31	3.2816	0.7226	0.1786	3.6392	-1.0699	2.2801	0.0952	-0.3407	-0.2939	0.1641	-0.1242	-0.3248	0.2397	0.2726	-0.0596	0.3113	-0.0016	0.0199	0.2459	-0.0258	0.2953	-15.1374	1.6943	100.6765
32	1.3285	0.5797	-0.0412	4.1502	-0.9224	0.9519	0.0171	-0.0147	0.0965	0.3885	-0.0671	-0.0851	-0.1893	0.1922	0.0556	0.261	-0.0524	-0.058	0.2673	-0.0059	0.2624	-12.8123	23.1511	99.4539

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 10:140 )	A	10 - 140
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 141:256 )	A	141 - 256
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 257:291 )	A	257 - 291
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 292:395 )	A	292 - 395
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 7:57 )	B	7 - 57
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 58:140 )	B	58 - 140
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 141:186 )	B	141 - 186
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 187:287 )	B	187 - 287
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 288:395 )	B	288 - 395
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 8:77 )	C	8 - 77
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 78:202 )	C	78 - 202
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 203:294 )	C	203 - 294
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 295:395 )	C	295 - 395
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 9:57 )	D	9 - 57
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 58:160 )	D	58 - 160
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 161:202 )	D	161 - 202
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 203:256 )	D	203 - 256
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 257:294 )	D	257 - 294
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 295:337 )	D	295 - 337
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 338:395 )	D	338 - 395
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 10:140 )	E	10 - 140
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 141:186 )	E	141 - 186
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 187:256 )	E	187 - 256
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 257:284 )	E	257 - 284
25	X-RAY DIFFRACTION	25	( CHAIN E AND RESID 285:395 )	E	285 - 395
26	X-RAY DIFFRACTION	26	( CHAIN F AND RESID 7:57 )	F	7 - 57
27	X-RAY DIFFRACTION	27	( CHAIN F AND RESID 58:92 )	F	58 - 92
28	X-RAY DIFFRACTION	28	( CHAIN F AND RESID 93:113 )	F	93 - 113
29	X-RAY DIFFRACTION	29	( CHAIN F AND RESID 114:186 )	F	114 - 186
30	X-RAY DIFFRACTION	30	( CHAIN F AND RESID 187:243 )	F	187 - 243
31	X-RAY DIFFRACTION	31	( CHAIN F AND RESID 244:294 )	F	244 - 294
32	X-RAY DIFFRACTION	32	( CHAIN F AND RESID 295:395 )	F	295 - 395

-
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