PDB-9zok: Crystal structure of Phosphoribosylaminoimidazole carboxylase fro...

ID or keywords:

Entry

Database: PDB / ID: 9zok

Title

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ADP complex)

Components

N5-carboxyaminoimidazole ribonucleotide synthase

Keywords

LYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Phosphoribosylaminoimidazole carboxylase

Function / homology

Function and homology information

5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Paraburkholderia xenovorans LB400 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / 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 Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ADP complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 15, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9zok.cif.gz	597.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9zok.ent.gz	490.5 KB	Display	PDB format
PDBx/mmJSON format	9zok.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9zok_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9zok_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9zok_validation.xml.gz	70.7 KB	Display
Data in CIF	9zok_validation.cif.gz	94.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zo/9zok ftp://data.pdbj.org/pub/pdb/validation_reports/zo/9zok	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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #192 - Dec 2015 Vancomycin similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: N5-carboxyaminoimidazole ribonucleotide synthase

B: N5-carboxyaminoimidazole ribonucleotide synthase

C: N5-carboxyaminoimidazole ribonucleotide synthase

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

1

A: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

2

B: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

3

C: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

4

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.914, 169.040, 170.130
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria) Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase

#1: Protein

N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase

Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Paraburkholderia xenovorans LB400 (bacteria)
Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase

-
Non-polymers , 7 types, 702 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H₂O

-
Details

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: 2.83 Å³/Da / Density % sol: 56.53 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ADP, plate 20558 E6 drop 2, Puck: ...Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ADP, plate 20558 E6 drop 2, Puck: PSL-1915, Cryo: 20% PEG 200 + 80% crystallant

Crystal

Density Matthews: 2.83 Å³/Da / Density % sol: 56.53 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ADP, plate 20558 E6 drop 2, Puck: ...

-
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: Nov 10, 2025
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: 2.09→47.09 Å / Num. obs: 114968 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.164 / R_pim(I) all: 0.046 / R_rim(I) all: 0.17 / Χ²: 1.1 / Net I/σ(I): 12.5 / Num. measured all: 1546549
Reflection shell	Resolution: 2.09→2.14 Å / % possible obs: 100 % / Redundancy: 13.4 % / R_merge(I) obs: 1.706 / Num. measured all: 112015 / Num. unique obs: 8370 / CC_1/2: 0.758 / R_pim(I) all: 0.482 / R_rim(I) all: 1.773 / Χ²: 0.97 / Net I/σ(I) obs: 1.6

-
Processing

Software

Name	Version	Classification
PHENIX	(2.0_5765: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.09→47.09 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2042	5605	4.88 %
R_work	0.168	-	-
obs	0.1697	114829	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→47.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11443	0	162	686	12291

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11994
X-RAY DIFFRACTION	f_angle_d	1.029	16383
X-RAY DIFFRACTION	f_dihedral_angle_d	12.572	4360
X-RAY DIFFRACTION	f_chiral_restr	0.058	1886
X-RAY DIFFRACTION	f_plane_restr	0.009	2153

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 (%)
2.09-2.11	0.3132	168	0.2873	3580	X-RAY DIFFRACTION	100
2.11-2.14	0.2707	162	0.2646	3605	X-RAY DIFFRACTION	100
2.14-2.16	0.2849	189	0.2425	3623	X-RAY DIFFRACTION	100
2.16-2.19	0.2796	157	0.2424	3591	X-RAY DIFFRACTION	100
2.19-2.22	0.2826	172	0.2278	3627	X-RAY DIFFRACTION	100
2.22-2.25	0.2209	180	0.2197	3595	X-RAY DIFFRACTION	100
2.25-2.28	0.2288	205	0.2024	3593	X-RAY DIFFRACTION	100
2.28-2.32	0.2369	186	0.195	3603	X-RAY DIFFRACTION	100
2.32-2.35	0.2511	200	0.1906	3564	X-RAY DIFFRACTION	100
2.35-2.39	0.2224	201	0.1887	3633	X-RAY DIFFRACTION	100
2.39-2.43	0.2163	168	0.184	3582	X-RAY DIFFRACTION	100
2.43-2.48	0.2205	194	0.1811	3646	X-RAY DIFFRACTION	100
2.48-2.53	0.2042	180	0.1772	3584	X-RAY DIFFRACTION	100
2.53-2.58	0.2277	213	0.1769	3620	X-RAY DIFFRACTION	100
2.58-2.63	0.2389	179	0.1916	3591	X-RAY DIFFRACTION	100
2.63-2.69	0.2384	192	0.1833	3642	X-RAY DIFFRACTION	100
2.69-2.76	0.2409	210	0.1963	3581	X-RAY DIFFRACTION	100
2.76-2.84	0.251	187	0.1823	3622	X-RAY DIFFRACTION	100
2.84-2.92	0.2103	195	0.1687	3652	X-RAY DIFFRACTION	100
2.92-3.01	0.2128	211	0.1634	3576	X-RAY DIFFRACTION	100
3.01-3.12	0.2125	207	0.1723	3622	X-RAY DIFFRACTION	100
3.12-3.25	0.2282	175	0.1816	3668	X-RAY DIFFRACTION	100
3.25-3.39	0.2035	159	0.1683	3668	X-RAY DIFFRACTION	100
3.39-3.57	0.1844	194	0.1544	3662	X-RAY DIFFRACTION	100
3.57-3.8	0.1863	170	0.1481	3694	X-RAY DIFFRACTION	100
3.8-4.09	0.1624	188	0.138	3661	X-RAY DIFFRACTION	100
4.09-4.5	0.1575	198	0.1214	3708	X-RAY DIFFRACTION	100
4.5-5.15	0.1422	197	0.1247	3731	X-RAY DIFFRACTION	100
5.15-6.49	0.2007	171	0.1608	3767	X-RAY DIFFRACTION	100
6.49-47.09	0.214	197	0.1788	3933	X-RAY DIFFRACTION	100

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	0.0825	0.2223	0.0122	0.5168	-0.1494	0.1034	-0.0098	-0.1391	0.1075	0.2702	0.0738	-0.0715	0.0124	0.1571	-0	0.3562	0.0148	-0.0172	0.3781	-0.0589	0.3352	-14.7022	41.9036	-13.3857
2	0.2413	0.0354	0.1122	0.1114	-0.0741	0.2454	0.0106	0.2021	0.299	-0.0936	-0.0494	-0.0092	-0.055	0.0943	0	0.3448	0.0015	-0.0004	0.375	0.0219	0.3317	-26.872	49.6459	-27.1233
3	0.3554	-0.1999	-0.2632	0.5792	0.0231	0.2965	0.0598	0.0245	-0.008	0.0814	-0.0696	0.15	-0.0177	0.0727	-0	0.3173	0.0205	-0.0267	0.3597	-0.0077	0.3191	-48.2472	43.859	-29.5451
4	0.8578	-0.2768	0.1008	0.7065	-0.2667	0.8604	0.0447	0.1272	-0.0981	-0.0781	-0.0383	0.0872	0.0718	-0.0663	0	0.2955	0.0185	-0.0128	0.3341	-0.0609	0.2681	-27.2439	28.7304	-23.9205
5	0.4128	-0.1281	0.1208	0.2579	-0.2415	0.2246	0.0045	0.0408	-0.1376	0.0219	-0.0219	0.3368	-0.0284	-0.1491	0	0.3316	-0.0003	0.0109	0.341	-0.0424	0.4038	-32.8459	22.7534	-12.4322
6	0.093	-0.1902	0.1733	0.2205	-0.1218	0.5215	-0.0911	-0.0458	-0.0372	0.1037	0.0868	-0.0221	-0.1141	0.2441	0	0.3959	0.0217	-0.0192	0.3793	-0.0263	0.3577	-12.1526	31.4042	0.7188
7	0.4066	-0.1067	0.2208	-0.0647	-0.2093	0.8613	-0.0201	-0.0274	-0.0324	0.1206	0.017	-0.017	-0.041	0.0608	0	0.3737	0.0055	-0.0263	0.3271	-0.0192	0.3467	-0.5104	18.6207	11.4834
8	0.1161	0.1151	0.1008	0.1231	0.0472	0.2155	0.0042	0.7256	0.2059	-0.1724	-0.0737	-0.1103	-0.2065	0.6442	-0.0007	0.3553	0.0061	-0.0343	0.6363	0.0008	0.3938	21.6108	10.1362	6.079
9	0.5991	0.0424	0.1565	0.5905	-0.4386	0.7517	0.0332	0.0352	-0.0908	0.0135	-0.0478	0.0164	0.114	0.0947	-0	0.324	0.0258	-0.0061	0.319	-0.0472	0.2974	-2.324	12.1966	-5.9664
10	0.8036	0.1715	-0.1675	0.3405	-0.3614	0.2604	0.0505	0.0509	-0.002	-0.1099	-0.0616	-0.0588	0.0071	0.1837	-0	0.3038	0.0227	0.0129	0.3928	-0.0417	0.3365	3.9831	27.8578	-20.1226
11	0.1977	0.3267	-0.0388	0.8178	0.2094	0.5236	-0.042	0.1483	-0.1713	0.1499	-0.0884	0.1102	0.3698	-0.0983	-0.0001	0.3904	-0.0033	0.0484	0.3612	-0.1042	0.3876	-3.6989	-20.7135	-50.252
12	0.841	-0.3786	-0.5292	0.193	0.047	0.6242	0.0062	-0.0322	0.2099	-0.0482	0.0474	-0.0499	-0.1036	0.0799	0	0.3451	-0.0191	0.0027	0.335	-0.0985	0.3804	13.4257	-4.1874	-49.4415
13	0.3449	0.0738	-0.1956	0.1733	-0.2884	0.3812	0.0169	-0.0684	0.0868	0.1037	-0.0837	-0.016	0.0177	0.4339	-0.0016	0.3543	0.102	-0.0329	0.5793	-0.1652	0.4253	13.0323	-12.3144	-25.9268
14	0.0546	-0.0352	-0.0308	0.1326	-0.0349	0.0773	0.1593	0.0744	-0.2791	-0.3107	-0.0668	0.4258	0.6585	-0.1553	0	0.6338	0.1013	-0.0365	0.4324	-0.0597	0.5765	-3.9208	-23.4039	-24.2045
15	0.2128	-0.2377	-0.0871	0.2724	0.11	0.4738	0.0982	-0.0932	-0.0338	-0.2295	-0.0614	0.2651	0.8612	-0.0042	-0.0335	0.8262	-0.0419	-0.0937	0.3116	-0.0593	0.6109	-9.7963	-31.9881	-22.0035
16	0.4859	0.1683	-0.1832	0.6623	-0.3029	0.7647	-0.0412	-0.0932	-0.5092	0.4674	0.0518	0.5864	0.6527	-0.5434	-0.0078	0.5268	-0.1913	0.1255	0.7428	0.0278	0.8082	-30.2121	-19.8974	-5.4425
17	0.5395	0.0018	0.6488	0.626	0.1491	1.224	0.0118	-0.1479	-0.0919	0.0822	-0.0533	0.0953	0.1087	-0.3338	-0	0.3669	0.0039	0.0003	0.457	-0.1186	0.4143	-16.8368	-8.9829	-15.9632
18	0.51	0.0035	0.2403	0.2053	-0.041	0.0512	0.0459	-0.0548	0.1834	-0.0265	-0.0854	0.0892	-0.0393	-0.1997	0	0.3519	0.0187	-0.0092	0.475	-0.126	0.4537	-22.9824	-6.2624	-36.9346

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 143 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 195 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 196 through 357 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 358 through 397 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 143 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 144 through 183 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 184 through 330 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 331 through 397 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 8 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 330 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 331 through 396 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 35 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 36 through 96 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 97 through 182 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 183 through 330 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 331 through 397 )

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 702 molecules

-
Details

-
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, 4 molecules ABCD

-Non-polymers , 7 types, 702 molecules

-Details

-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, 4 molecules ABCD

-
Non-polymers , 7 types, 702 molecules

-
Details

-
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