PDB-4nhe: The crystal structure of oxidoreductase (Gfo/Idh/MocA family) fro...

ID or keywords:

Entry

Database: PDB / ID: 4nhe

Title

The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP

Components

Oxidoreductase, Gfo/Idh/MocA family

Keywords

OXIDOREDUCTASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP.
Authors: Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Nov 4, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4nhe.cif.gz	410.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4nhe.ent.gz	338.3 KB	Display	PDB format
PDBx/mmJSON format	4nhe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4nhe_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4nhe_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4nhe_validation.xml.gz	43.5 KB	Display
Data in CIF	4nhe_validation.cif.gz	62 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhe ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhe	HTTPS FTP

-
Related structure data

Related structure data	4iq0S 2ho5 S: Starting model for refinement
Similar structure data	3g6d-d 6txz-3 3hfm-d 4qfc-d 2poq-1 6p4a-d 3ip3-2 4htg-2 5a03-2 2p19-d 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: MCSG-APC111382

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Oxidoreductase, Gfo/Idh/MocA family

B: Oxidoreductase, Gfo/Idh/MocA family

C: Oxidoreductase, Gfo/Idh/MocA family

hetero molecules

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

1

A: Oxidoreductase, Gfo/Idh/MocA family

B: Oxidoreductase, Gfo/Idh/MocA family

hetero molecules

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

2

C: Oxidoreductase, Gfo/Idh/MocA family

hetero molecules

C: Oxidoreductase, Gfo/Idh/MocA family

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.768, 195.905, 349.301
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	22
Space group name H-M	F222

Components on special symmetry positions

ID	Model	Components
1	1	C-710- HOH

Details

experimentally unknown. The chains A and B are predicted to form a dimer. The chain C and its symmetry-related molecule (-x,-y,z) are predicted to form a dimer.

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Oxidoreductase, Gfo/Idh/MocA family Mass: 36683.262 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1482 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q97PV8, UniProt: A0A0H2UR04*PLUS

#1: Protein

Oxidoreductase, Gfo/Idh/MocA family

Mass: 36683.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1482 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q97PV8, UniProt: A0A0H2UR04*PLUS

-
Non-polymers , 5 types, 644 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 624 / 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: 3.8 Å³/Da / Density % sol: 67.63 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Sodium Acetate:HCl, 3.5M sodium format, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.95→36.5 Å / Num. all: 117182 / Num. obs: 117182 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 4.7 % / R_merge(I) obs: 0.081 / Net I/σ(I): 28
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.731 / Mean I/σ(I) obs: 1.52 / Num. unique all: 5848 / % possible all: 98.4

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY:4IQ0

4iq0

Resolution: 1.95→36.174 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2067	5837	5.03 %	random
R_work	0.1759	-	-	-
obs	0.1774	116005	95.62 %	-
all	-	116005	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→36.174 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7650	0	205	624	8479

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8058
X-RAY DIFFRACTION	f_angle_d	1.05	10953
X-RAY DIFFRACTION	f_dihedral_angle_d	14.423	2862
X-RAY DIFFRACTION	f_chiral_restr	0.073	1210
X-RAY DIFFRACTION	f_plane_restr	0.004	1397

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 (%)
1.9496-1.9718	0.297	173	0.2777	2999	X-RAY DIFFRACTION	80
1.9718-1.995	0.3079	242	0.2694	3710	X-RAY DIFFRACTION	98
1.995-2.0193	0.2706	203	0.2607	3702	X-RAY DIFFRACTION	98
2.0193-2.0449	0.2706	217	0.2584	3755	X-RAY DIFFRACTION	98
2.0449-2.0718	0.2855	195	0.2371	3727	X-RAY DIFFRACTION	98
2.0718-2.1002	0.2556	212	0.2303	3699	X-RAY DIFFRACTION	98
2.1002-2.1302	0.2592	183	0.2283	3726	X-RAY DIFFRACTION	97
2.1302-2.162	0.2487	214	0.2216	3670	X-RAY DIFFRACTION	97
2.162-2.1957	0.2615	186	0.2151	3707	X-RAY DIFFRACTION	97
2.1957-2.2317	0.2263	178	0.2174	3709	X-RAY DIFFRACTION	96
2.2317-2.2702	0.2591	201	0.2129	3636	X-RAY DIFFRACTION	96
2.2702-2.3115	0.2688	176	0.2154	3638	X-RAY DIFFRACTION	95
2.3115-2.3559	0.2511	191	0.2247	3685	X-RAY DIFFRACTION	96
2.3559-2.404	0.2832	217	0.2225	3599	X-RAY DIFFRACTION	95
2.404-2.4563	0.2932	187	0.2214	3634	X-RAY DIFFRACTION	95
2.4563-2.5134	0.2777	199	0.2123	3608	X-RAY DIFFRACTION	95
2.5134-2.5762	0.2676	169	0.2091	3648	X-RAY DIFFRACTION	95
2.5762-2.6459	0.243	185	0.2075	3607	X-RAY DIFFRACTION	94
2.6459-2.7237	0.2422	194	0.2112	3612	X-RAY DIFFRACTION	94
2.7237-2.8116	0.2486	187	0.2009	3571	X-RAY DIFFRACTION	93
2.8116-2.912	0.2417	187	0.1955	3620	X-RAY DIFFRACTION	95
2.912-3.0286	0.2274	199	0.1959	3634	X-RAY DIFFRACTION	94
3.0286-3.1663	0.2324	187	0.1895	3655	X-RAY DIFFRACTION	95
3.1663-3.3332	0.2175	199	0.1733	3751	X-RAY DIFFRACTION	97
3.3332-3.5418	0.1796	193	0.1565	3789	X-RAY DIFFRACTION	98
3.5418-3.815	0.1936	180	0.1446	3799	X-RAY DIFFRACTION	98
3.815-4.1984	0.1453	198	0.1294	3774	X-RAY DIFFRACTION	97
4.1984-4.8047	0.1338	189	0.1191	3698	X-RAY DIFFRACTION	95
4.8047-6.0489	0.152	188	0.1438	3910	X-RAY DIFFRACTION	99
6.0489-36.1798	0.1785	208	0.1686	3896	X-RAY DIFFRACTION	96

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	4.6923	0.4646	-0.1972	5.3556	-2.1869	6.8917	-0.2092	-0.071	0.3943	0.6251	0.0694	-0.7323	-0.622	1.0718	0.1025	0.4563	-0.0269	-0.2043	0.5091	-0.1017	0.3991	22.3848	74.272	70.2679
2	4.0643	0.1324	-1.008	2.4533	-1.2293	7.2786	-0.2287	-0.9581	0.3672	0.8176	0.1565	-0.479	-0.5063	0.0641	0.0481	0.6597	0.051	-0.2455	0.5801	-0.0929	0.4807	21.8296	72.7917	80.2747
3	1.891	-0.2379	0.1972	1.8658	0.0812	3.0257	-0.196	-0.4103	0.4556	0.3803	0.0825	-0.0618	-0.6641	0.0267	0.0989	0.4238	0.1278	-0.0902	0.3048	-0.0541	0.3567	8.5681	75.4841	63.2841
4	5.143	-1.07	-0.1503	6.1755	0.9936	4.2634	-0.0792	-0.7696	-0.0953	0.7861	-0.0394	0.0224	0.1936	0.2874	0.1045	0.3499	0.1243	-0.0148	0.4738	0.0055	0.2203	12.2929	50.942	68.271
5	2.1031	-0.1192	0.0118	3.0373	-0.5683	2.2814	-0.0777	-0.0927	0.122	-0.0053	-0.0418	0.1405	-0.1493	-0.1693	0.0961	0.1755	0.1074	-0.0144	0.2618	-0.0491	0.2056	3.9335	60.8155	54.6152
6	2.3533	0.7145	1.1493	3.7489	2.7244	7.7045	-0.0862	0.1844	0.2719	-0.1833	0.0897	-0.3444	-0.5175	0.767	-0.0612	0.237	-0.0026	-0.0147	0.28	0.119	0.3411	17.8211	71.5846	46.526
7	2.7287	0.5553	0.3089	4.8663	-0.0752	1.8233	-0.2128	-0.0958	0.2769	0.2038	0.0236	0.2453	-0.493	-0.4532	0.1382	0.3528	0.2075	-0.032	0.3869	-0.079	0.3271	-0.2853	70.1144	60.4173
8	2.753	0.3746	0.6551	4.4878	-0.5564	6.1202	-0.0225	0.5541	-0.0931	-0.5488	0.232	0.0716	0.1972	-0.1111	-0.1861	0.3381	0.041	-0.0172	0.4422	-0.0419	0.1613	1.7761	36.3342	11.4406
9	0.6703	0.5818	0.3796	1.0349	0.6271	1.5155	0.0385	0.1122	-0.0401	-0.114	0.0319	0.0932	-0.047	-0.0775	-0.0818	0.2127	0.1093	-0.0133	0.2764	-0.0023	0.2107	2.1872	42.9011	35.1731
10	5.2583	2.356	1.8067	1.1925	0.8817	5.339	-0.1388	-0.7869	-0.0544	0.5385	0.1057	0.2325	0.1939	-0.0933	0.0219	0.3659	0.1964	0.0914	0.3979	0.0109	0.3992	-29.0301	18.3984	52.6932
11	5.7863	0.9282	1.4572	0.3471	-0.2019	2.9114	-0.1145	-0.5379	-0.234	0.2186	0.0998	0.3869	-0.2537	-0.584	0.0859	0.3887	0.1683	0.1298	0.4135	0.0221	0.5233	-38.3396	16.1852	49.772
12	5.5307	-0.1686	-1.1565	3.9392	0.4571	3.282	-0.2054	0.0566	0.3675	0.1547	-0.0509	0.4486	-0.1953	-0.3973	0.1097	0.3002	0.1034	0.0537	0.3531	-0.048	0.4529	-34.0323	21.0719	41.6325
13	4.9006	0.261	-1.4727	2.0922	0.3861	3.0235	-0.103	0.2018	0.1279	-0.0449	0.1047	0.2032	0.0144	-0.196	0.0733	0.259	0.1283	-0.0182	0.2779	-0.0255	0.3052	-23.6868	20.0923	34.6409
14	4.199	-1.1497	0.7344	1.7925	-0.2027	1.1938	-0.1752	-0.3183	0.3812	0.2092	0.1417	-0.1875	-0.1961	-0.0534	0.0301	0.271	0.0991	-0.0009	0.2238	-0.0524	0.2985	-6.2265	17.7614	47.4978
15	4.5819	-2.0256	3.5484	5.1683	-0.3485	7.7053	0.0502	-0.9044	-0.6734	-0.127	0.1265	1.0834	-0.0314	-1.0824	-0.2011	0.232	0.0599	0.0381	0.3972	0.0532	0.5947	-23.3203	-5.4725	43.6616
16	2.2191	0.281	-0.3499	2.2548	0.0478	1.1853	-0.0233	0.113	-0.0651	-0.0846	0.057	0.0921	-0.0395	-0.1116	0.0014	0.2686	0.117	-0.0158	0.2701	-0.0241	0.3325	-10.7513	5.2365	37.1711
17	1.2195	-0.2156	0.2381	0.9693	0.1933	0.6125	-0.0795	-0.3441	0.0499	0.1758	-0.001	-0.1448	-0.0156	-0.021	0.0433	0.2857	0.0997	-0.0214	0.2976	-0.0185	0.3768	0.2826	6.3218	46.1095
18	9.951	0.8628	0.5818	2.4029	0.4929	3.1814	-0.135	-0.7991	-0.3678	0.4375	0.1922	-0.3511	-0.0569	0.3053	-0.0568	0.4233	0.1579	-0.0619	0.3433	-0.0234	0.371	2.5462	10.6435	57.5038
19	2.8794	-1.26	0.5541	2.9194	-2.5657	2.4858	-0.2628	-0.4652	0.2236	0.7608	0.3821	-0.0182	-0.5271	-0.3339	-0.1132	0.448	0.1809	0.0026	0.4549	-0.1573	0.347	-15.5888	23.0151	54.009
20	1.5825	0.142	-0.3041	5.6991	1.3458	1.2407	-0.0607	0.1319	0.1022	-0.2516	-0.0412	0.3123	-0.0971	-0.1015	0.1271	0.2339	0.1148	-0.021	0.2741	0.0002	0.2663	-13.249	14.1075	33.3047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 148 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 149 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 235 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 236 through 292 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 293 through 325 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 71 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 72 through 325 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 0 through 23 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 24 through 54 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 55 through 71 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 72 through 112 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 113 through 148 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 149 through 166 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 167 through 216 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 217 through 247 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 248 through 267 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 268 through 292 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 293 through 325 )

-
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://pdbjlvh1.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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 644 molecules

-
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

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 5 types, 644 molecules

-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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 644 molecules

-
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