PDB-9bld: crystal structure of thermostable dienelactone hydrolase

ID or keywords:

Entry

Database: PDB / ID: 9bld

Title

crystal structure of thermostable dienelactone hydrolase

Components

Carboxymethylenebutenolidase

Keywords

HYDROLASE / Dienelactone hydrolase / esterase activity / PETase / BHETase / thermostable enzyme / PET depolymerization

Function / homology

: / Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / Carboxymethylenebutenolidase

Function and homology information

Biological species

Hydrogenobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

Muniz, J.R.C. / Almeida, D. / Brito, V. / Ciancaglini, I. / Sandano, A.L.H. / Squina, F. / Garcia, W.

Funding support

Brazil, 25items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2020/15595-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2020/05784-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2022/05731-2	Brazil
Sao Paulo Research Foundation (FAPESP)	2022/08958-8	Brazil
Sao Paulo Research Foundation (FAPESP)	2015/23279-6	Brazil
Sao Paulo Research Foundation (FAPESP)	2019/19360-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2020/11019-8	Brazil
Sao Paulo Research Foundation (FAPESP)	2021/04254-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2022/14112-4	Brazil
Sao Paulo Research Foundation (FAPESP)	2023/04782-5	Brazil
Sao Paulo Research Foundation (FAPESP)	2023/04828-5	Brazil
Sao Paulo Research Foundation (FAPESP)	2023/12398-0	Brazil
Sao Paulo Research Foundation (FAPESP)	2023/04941-6	Brazil
Sao Paulo Research Foundation (FAPESP)	2023/08832-7	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	305816/2020-9	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	422132/2018-7	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	306279/2020-7	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	315847/2021-2	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	403844/2023-1	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	176662/2023-5	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	304998/2023-0	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	307199/2023-1	Brazil
Other government	88887.625460/2021-00	Brazil
Other government	88887.600186/2021-00	Brazil
Other government	88887.518696/2020-00	Brazil

Citation

Journal: To Be Published
Title: crystal structure of thermostable dienelactone hydrolase
Authors: Muniz, J.R.C. / Almeida, D. / Brito, V. / Ciancaglini, I. / Sandano, A.L.H. / Squina, F. / Garcia, W.

History

Deposition	Apr 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9bld.cif.gz	508.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bld.ent.gz	320.4 KB	Display	PDB format
PDBx/mmJSON format	9bld.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/9bld ftp://data.pdbj.org/pub/pdb/validation_reports/bl/9bld	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

Deposited unit

A: Carboxymethylenebutenolidase

B: Carboxymethylenebutenolidase

C: Carboxymethylenebutenolidase

D: Carboxymethylenebutenolidase

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

1

A: Carboxymethylenebutenolidase

B: Carboxymethylenebutenolidase

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

2

C: Carboxymethylenebutenolidase

D: Carboxymethylenebutenolidase

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

Unit cell

Length a, b, c (Å)	77.385, 87.298, 143.245
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	THR	THR	1 - 234	7 - 240
2	1	1	MET	MET	THR	THR	1 - 234	7 - 240
3	2	2	GLY	GLY	LEU	LEU	2 - 233	8 - 239
4	2	2	GLY	GLY	LEU	LEU	2 - 233	8 - 239
5	3	3	MET	MET	THR	THR	1 - 234	7 - 240
6	3	3	MET	MET	THR	THR	1 - 234	7 - 240
7	4	4	GLY	GLY	LEU	LEU	2 - 233	8 - 239
8	4	4	GLY	GLY	LEU	LEU	2 - 233	8 - 239
9	5	5	MET	MET	THR	THR	1 - 234	7 - 240
10	5	5	MET	MET	THR	THR	1 - 234	7 - 240
11	6	6	GLY	GLY	LEU	LEU	2 - 233	8 - 239
12	6	6	GLY	GLY	LEU	LEU	2 - 233	8 - 239

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Carboxymethylenebutenolidase Mass: 27259.045 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria) Gene: HTH_1817 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DKA9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.54 % / Description: long rods
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium formate, 0.1 M of bis-tris propane pH 7.5, and 20% w/v of PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97718 Å / Relative weight: 1
Reflection	Resolution: 1.67→74.545 Å / Num. obs: 113000 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.995 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.035 / R_rim(I) all: 0.128 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.67→1.699 Å / Redundancy: 12.7 % / R_merge(I) obs: 3.785 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5592 / CC_1/2: 0.363 / R_pim(I) all: 1.095 / R_rim(I) all: 3.942 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.67→74.545 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.967 / SU B: 4.785 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1891	5771	5.112 %
R_work	0.1641	107121	-
all	0.165	-	-
obs	-	112892	99.868 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.315 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.446 Å²	-0 Å²	-0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.466 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→74.545 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7410	0	0	768	8178

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7734
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7119
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.827	10496
X-RAY DIFFRACTION	r_angle_other_deg	0.553	1.754	16442
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.69	5	969
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.121	5	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.447	10	1249
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.696	10	367
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1094
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	9145
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1843
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1365
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	5985
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	3820
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	3699
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	626
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.128	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.161	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.149	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.199	0.2	17
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.011	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.951	1.859	3774
X-RAY DIFFRACTION	r_mcbond_other	1.951	1.859	3774
X-RAY DIFFRACTION	r_mcangle_it	2.86	3.334	4720
X-RAY DIFFRACTION	r_mcangle_other	2.862	3.334	4721
X-RAY DIFFRACTION	r_scbond_it	3.305	2.281	3960
X-RAY DIFFRACTION	r_scbond_other	3.305	2.281	3961
X-RAY DIFFRACTION	r_scangle_it	5.237	3.996	5757
X-RAY DIFFRACTION	r_scangle_other	5.237	3.996	5758
X-RAY DIFFRACTION	r_lrange_it	7.132	22.29	8936
X-RAY DIFFRACTION	r_lrange_other	7.032	21.064	8724
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.07	0.05	7640
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.069	0.05	7569
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.079	0.05	7610
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	7591
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.074	0.05	7589
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.083	0.05	7517

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07042	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07042	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06948	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06948	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.0789	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.0789	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06539	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06539	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07395	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07395	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08346	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08346	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.67-1.714	0.351	411	0.346	7777	0.346	8303	0.894	0.895	98.615	0.344
1.714-1.76	0.308	450	0.308	7599	0.308	8052	0.934	0.933	99.9627	0.305
1.76-1.811	0.306	416	0.277	7414	0.279	7831	0.94	0.948	99.9872	0.27
1.811-1.867	0.266	402	0.242	7206	0.243	7608	0.953	0.961	100	0.226
1.867-1.928	0.23	378	0.209	7011	0.21	7389	0.965	0.971	100	0.189
1.928-1.996	0.222	357	0.189	6793	0.19	7150	0.968	0.977	100	0.164
1.996-2.071	0.217	344	0.177	6575	0.179	6919	0.969	0.98	100	0.154
2.071-2.156	0.189	337	0.159	6330	0.161	6667	0.978	0.985	100	0.14
2.156-2.252	0.177	324	0.158	6064	0.159	6388	0.981	0.985	100	0.138
2.252-2.361	0.186	315	0.146	5821	0.148	6136	0.978	0.987	100	0.129
2.361-2.489	0.17	291	0.142	5536	0.143	5828	0.983	0.988	99.9828	0.127
2.489-2.64	0.184	283	0.148	5223	0.149	5506	0.98	0.987	100	0.137
2.64-2.822	0.194	258	0.15	4958	0.153	5217	0.977	0.986	99.9808	0.142
2.822-3.047	0.189	243	0.161	4616	0.163	4859	0.977	0.984	100	0.16
3.047-3.338	0.175	222	0.155	4266	0.156	4488	0.981	0.986	100	0.16
3.338-3.731	0.178	205	0.153	3868	0.154	4073	0.981	0.987	100	0.165
3.731-4.306	0.148	198	0.138	3442	0.138	3640	0.986	0.989	100	0.161
4.306-5.27	0.137	150	0.119	2938	0.12	3088	0.991	0.993	100	0.146
5.27-7.434	0.193	96	0.164	2333	0.165	2429	0.978	0.986	100	0.193
7.434-74.545	0.194	91	0.184	1351	0.184	1442	0.984	0.978	100	0.219

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	2.0982	-2.3553	-4.1846	2.6986	4.7015	8.3809	0.1932	0.0288	0.1634	-0.2593	0.0614	-0.2203	-0.3248	0.0116	-0.2546	0.1838	-0.0546	0.0278	0.2008	0.0286	0.127	20.2865	-3.9962	-40.0744
2	1.3853	0.7007	0.1517	1.044	0.2962	2.2526	-0.0195	0.1828	0.1248	-0.0436	0.0896	-0.0037	-0.0967	-0.123	-0.0701	0.106	0.0025	-0.0279	0.1499	0.0419	0.0463	14.5284	-2.9652	-28.8869
3	12.6065	-0.1966	-0.3336	0.3023	-0.3229	2.022	-0.3143	0.004	-0.6806	-0.3459	0.1139	0.0613	0.4634	-0.1696	0.2004	0.4245	-0.1172	-0.0371	0.15	-0.0223	0.0896	9.8987	-18.6696	-34.3827
4	0.4844	0.1428	-0.3758	0.0541	-0.1423	1.4413	-0.1357	0.0486	0.0648	-0.0276	0.0466	0.0223	0.1661	0.0288	0.0891	0.1067	0.0078	0.0073	0.1234	0.0015	0.0531	17.6778	-12.2768	-18.5257
5	10.0958	1.9661	-7.2212	0.7456	-0.9162	6.62	0.0863	-0.3038	0.3547	0.1563	0.0509	0.0131	0.239	0.2262	-0.1372	0.1795	-0.0131	0.0023	0.1608	-0.0375	0.0712	17.5494	-1.6537	26.1264
6	0.7217	-0.716	-0.0136	2.7072	-0.6374	1.8351	0.0416	-0.0555	0.1284	0.1244	0.0224	-0.0266	0.1078	0.233	-0.064	0.1242	0.0063	-0.0118	0.1625	-0.0049	0.0355	22.4934	-4.6746	14.668
7	1.683	-1.0627	-0.6565	3.1391	1.5117	1.1916	0.0179	-0.1869	-0.1524	0.3945	-0.1193	0.2769	0.3364	0.0053	0.1013	0.2236	-0.0132	0.0146	0.1316	0.0127	0.0333	12.8756	-12.4634	21.913
8	0.3164	-0.0919	-0.3324	0.3022	0.2935	0.9085	-0.0125	-0.0033	0.0623	0.0747	-0.0375	0.0371	0.1522	0.054	0.05	0.1168	0.0246	0.0351	0.1109	0.021	0.0535	13.5553	-10.4559	4.7713
9	1.8809	-0.8262	2.6065	0.3935	-1.2657	4.3434	0.1725	0.2015	-0.2914	-0.061	0.0022	0.1067	0.113	0.1187	-0.1748	0.1077	-0.0307	-0.037	0.1973	-0.0409	0.1226	-21.8525	-1.1587	-24.1114
10	1.6173	0.1614	0.0178	1.7326	-0.4578	1.5071	-0.0385	0.2036	0.0187	-0.0162	0.0336	-0.0599	-0.0407	0.2379	0.0048	0.0874	-0.0195	0.0091	0.155	-0.0093	0.0692	-14.7281	6.3315	-17.0809
11	1.5204	1.8023	-0.0945	4.5649	-0.7589	0.6513	0.0279	0.2401	-0.0068	-0.0734	-0.1309	-0.0677	-0.1431	-0.0369	0.103	0.1381	0.0059	-0.0336	0.2154	0.0107	0.0421	-24.7848	11.4082	-23.757
12	0.6734	0.0675	0.0065	0.2682	0.3822	0.6867	-0.0892	0.0158	-0.0007	-0.0184	0.0727	0.0105	-0.0375	0.0046	0.0165	0.0669	-0.0218	-0.0096	0.119	0.0308	0.0954	-21.8866	11.7903	-5.9215
13	0.6797	0.253	0.4258	0.5251	-0.2751	0.8992	0.0898	-0.147	-0.0967	0.0013	0.0152	-0.06	-0.0183	-0.2038	-0.1049	0.0752	-0.0091	0.0214	0.154	0.0039	0.0658	-20.3719	3.2591	29.133
14	0.8614	-0.3232	0.2896	1.1946	-0.4053	1.1934	0.1188	-0.2094	0.1046	0.3118	-0.1938	-0.0234	-0.2193	-0.0461	0.075	0.1967	-0.0677	0.0092	0.1857	-0.0528	0.0401	-18.2719	15.1458	33.603
15	0.376	0.101	-0.027	1.436	-0.244	0.5934	-0.0295	-0.0677	-0.0212	0.0748	-0.0222	-0.0405	-0.1481	0.0759	0.0517	0.0847	-0.006	0.0004	0.1327	-0.017	0.0734	-11.3521	11.581	20.8271
16	0.8135	0.0568	0.495	0.1445	-0.2022	0.9113	-0.0786	0.0087	0.0307	-0.0544	0.0768	0.0328	-0.0447	-0.058	0.0017	0.0739	-0.0113	-0.0115	0.14	-0.0081	0.0954	-22.1896	14.1029	11.7911

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 12
2	X-RAY DIFFRACTION	2	ALL	A	13 - 68
3	X-RAY DIFFRACTION	3	ALL	A	69 - 92
4	X-RAY DIFFRACTION	4	ALL	A	93 - 234

-
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