PDB-6vdt: Crystal Structure of Dehaloperoxidase B in Complex with cofactor ...

ID or keywords:

Entry

Database: PDB / ID: 6vdt

Title

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-nitrophenol

Components

Dehaloperoxidase B

Keywords

OXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding

Function / homology

Function and homology information

oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Amphitrite ornata (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.978 Å

Authors

Ghiladi, R.A. / de Serrano, V.S. / McGuire, A. / Malewschik, T.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
Authors: McGuire, A.H. / Petit, A.R. / Kang, J. / Malewschik, T. / de Serrano, V. / Carey, L.M. / Ghiladi, R.A.

History

Deposition	Dec 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 30, 2021	Group: Data collection / Category: pdbx_reflns_twin Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.2	Oct 11, 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 / pdbx_validate_chiral Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vdt.cif.gz	138.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6vdt.ent.gz	106.9 KB	Display	PDB format
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Validation report

Summary document	6vdt_validation.pdf.gz	484.2 KB	Display	wwPDB validaton report
Full document	6vdt_full_validation.pdf.gz	500.6 KB	Display
Data in XML	6vdt_validation.xml.gz	3.4 KB	Display
Data in CIF	6vdt_validation.cif.gz	7.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vd/6vdt ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vdt	HTTPS FTP

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Related structure data

Related structure data	6vd3C 6vd4C 6vd5C 6vd6C 6vdrC 6vdsC 6vduC 6vdvC 6vdwC 6vdxC 6vdyC 3ixfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vds-2 6ch5-1 6ch5-2 6vdy-1 6oo6-1 6oo8-1 4kmw-1 6vd6-1 6vd4-1 4hsx-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (2) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#116 - Aug 2009
Sulfotransferases
similarity (1)
#206 - Feb 2017
Globin Evolution
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (2)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: Dehaloperoxidase B

B: Dehaloperoxidase B

hetero molecules

32.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dehaloperoxidase B

hetero molecules

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

2

B: Dehaloperoxidase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.700, 67.660, 67.730
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Dehaloperoxidase B Mass: 15414.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) pLysS / References: UniProt: Q9NAV7

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Non-polymers , 6 types, 132 molecules

#2: Chemical	ChemComp-FDE / FE(III) DEUTEROPORPHYRIN IX Mass: 564.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₀H₂₈FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NPO / P-NITROPHENOL Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅NO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.86 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulphate MPEG 2000, 29-33%

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 1 Å

Detector

Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 4, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.6286
pseudo-merohedral	1	1	-H, -L, -K	2	0.3714

Reflection

Resolution: 1.77→47.99 Å / Num. obs: 25924 / % possible obs: 95.57 % / Redundancy: 4.2 % / CC_1/2: 0.999 / Net I/σ(I): 20.9

Reflection shell

Resolution: 1.77→1.82 Å / Num. unique obs: 1325 / CC_1/2: 0.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf

Resolution: 1.978→37.097 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.908 / SU B: 7.579 / SU ML: 0.118 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2229	932	5.153 %
R_work	0.167	-	-
all	0.17	-	-
obs	-	18087	93.126 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.366 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.816 Å²	0 Å²	0 Å²
2-	-	-3.008 Å²	-0 Å²
3-	-	-	-6.808 Å²

Refinement step

Cycle: LAST / Resolution: 1.978→37.097 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2134	0	113	124	2371

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2798
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	2458
X-RAY DIFFRACTION	r_angle_refined_deg	2.384	1.696	3857
X-RAY DIFFRACTION	r_angle_other_deg	1.466	1.618	5770
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.101	5	378
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.614	22.876	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.699	15	497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.29	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.14	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3418
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	646
X-RAY DIFFRACTION	r_nbd_refined	0.275	0.2	825
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	2303
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1286
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1073
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.218	0.2	161
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.192	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.215	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.369	1.842	1339
X-RAY DIFFRACTION	r_mcbond_other	1.368	1.84	1338
X-RAY DIFFRACTION	r_mcangle_it	2.263	2.76	1740
X-RAY DIFFRACTION	r_mcangle_other	2.263	2.762	1741
X-RAY DIFFRACTION	r_scbond_it	1.608	2.207	1459
X-RAY DIFFRACTION	r_scbond_other	1.591	2.197	1449
X-RAY DIFFRACTION	r_scangle_it	2.434	3.337	2099
X-RAY DIFFRACTION	r_scangle_other	2.427	3.329	2087
X-RAY DIFFRACTION	r_lrange_it	7.378	24.524	3521
X-RAY DIFFRACTION	r_lrange_other	7.35	24.483	3508

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 (%)
1.978-2.03	0.346	66	0.234	1286	X-RAY DIFFRACTION	96.3649
2.03-2.085	0.335	49	0.18	939	X-RAY DIFFRACTION	70.8752
2.085-2.145	0.221	55	0.166	1252	X-RAY DIFFRACTION	99.2407
2.145-2.211	0.248	53	0.167	1225	X-RAY DIFFRACTION	100.7092
2.211-2.283	0.269	55	0.167	838	X-RAY DIFFRACTION	69.4401
2.283-2.363	0.232	58	0.135	1170	X-RAY DIFFRACTION	100.3268
2.363-2.452	0.149	58	0.131	1117	X-RAY DIFFRACTION	99.915
2.452-2.552	0.196	63	0.125	1079	X-RAY DIFFRACTION	99.5641
2.552-2.665	0.172	50	0.151	1051	X-RAY DIFFRACTION	100.182
2.665-2.794	0.196	41	0.163	816	X-RAY DIFFRACTION	82.5626
2.794-2.944	0.199	57	0.171	968	X-RAY DIFFRACTION	99.9025
2.944-3.122	0.289	52	0.17	868	X-RAY DIFFRACTION	100
3.122-3.335	0.159	52	0.165	842	X-RAY DIFFRACTION	100
3.335-3.6	0.208	35	0.179	715	X-RAY DIFFRACTION	87.925
3.6-3.94	0.188	27	0.16	549	X-RAY DIFFRACTION	75
3.94-4.399	0.256	35	0.133	676	X-RAY DIFFRACTION	100.2821
4.399-5.068	0.156	33	0.162	600	X-RAY DIFFRACTION	99.8423
5.068-6.178	0.231	43	0.22	507	X-RAY DIFFRACTION	99.6377
6.178-8.618	0.382	30	0.214	407	X-RAY DIFFRACTION	99.5444
8.618-37.097	0.241	20	0.236	250	X-RAY DIFFRACTION	98.5401

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	0.9811	-0.5915	0.266	0.4527	-0.3912	0.6944	-0.027	0.0115	-0.0797	0.0573	-0.01	0.0515	-0.1006	0.0616	0.037	0.0663	-0.0048	0.0032	0.0804	0.0164	0.0929	-0.0264	-1.5742	-23.8675
2	5.0535	-0.8114	5.2086	0.5426	-0.7129	5.4056	-0.0512	0.1397	0.3213	0.0629	-0.2329	-0.2237	-0.037	0.0787	0.2841	0.0312	-0.0397	-0.0298	0.1342	0.0714	0.1419	15.7377	-5.0262	-16.1528
3	2.8526	1.559	0.4786	0.8547	0.2616	0.0809	-0.0475	0.0316	0.0598	-0.0327	0.0317	0.0283	-0.0102	0.0049	0.0158	0.0834	-0.0142	-0.0269	0.0862	-0.0329	0.0666	11.3869	-1.0885	-7.7911
4	0.576	-0.9681	-0.0161	4.0209	0.2037	1.5542	-0.2894	-0.0757	0.0058	0.3888	0.2362	0.1528	0.0296	0.0029	0.0532	0.1564	0.04	0.0111	0.0675	0.0237	0.0608	2.8829	-5.0058	-10.7364
5	2.1489	1.457	-1.3604	1.7412	-1.7221	1.7107	0.3292	-0.1059	0.161	0.1443	-0.1426	0.1921	-0.1226	0.1368	-0.1866	0.0903	-0.0329	0.0244	0.0926	-0.0286	0.071	2.339	12.904	-25.1607
6	3.5113	-4.6858	-3.1594	6.2588	4.219	2.8595	-0.2269	-0.0414	-0.2056	0.2813	0.0581	0.2865	0.179	0.0646	0.1688	0.1331	-0.0743	-0.0451	0.0964	0.0198	0.1075	8.9313	13.5743	-12.488
7	3.2789	3.5908	-0.5337	4.3957	-2.1519	5.3952	0.2374	-0.1378	0.0075	0.3548	-0.3142	-0.0244	-0.3116	0.5347	0.0768	0.1119	-0.0758	-0.0882	0.0839	0.0609	0.1067	15.2376	5.7694	-18.9093
8	1.4075	0.5972	1.4711	3.8184	2.3201	2.3489	0.0083	0.3768	0.1501	0.225	-0.2318	0.1536	0.1044	0.209	0.2235	0.0524	-0.0255	-0.0004	0.149	0.0478	0.0983	8.3242	-3.2946	-28.0447
9	2.0345	2.8391	1.295	4.6568	1.1515	1.6319	0.0171	0.0267	-0.0156	0.0309	-0.2018	-0.1669	0.0673	0.143	0.1847	0.0384	-0.0296	0.0101	0.1357	0.0266	0.0841	7.1131	3.3734	-32.0245
10	1.0977	-0.6253	2.8616	2.5723	-2.1678	7.6339	0.019	-0.0022	0.0325	0.2012	-0.2063	-0.5749	0.0997	-0.0147	0.1874	0.1895	-0.133	-0.1049	0.0959	0.0818	0.1669	14.2907	15.1292	-21.7789
11	0.5611	0.3087	-0.442	0.6237	-0.4963	0.817	-0.0502	-0.0522	-0.0242	-0.0461	0.0582	-0.0512	0.0562	0.0232	-0.008	0.0601	-0.009	-0.0161	0.0739	0.001	0.0918	-17.1979	6.7463	-14.9111
12	1.7882	-0.7918	3.455	6.6677	-1.2252	6.6911	-0.0292	-0.1404	-0.0658	-0.1288	0.1252	0.5313	-0.0573	-0.2742	-0.096	0.0429	-0.0232	0.016	0.095	-0.0637	0.1287	-27.5398	-8.0076	-12.9217
13	6.8467	1.7605	-4.0378	1.9018	-1.4874	2.6199	-0.106	-0.1154	-0.4052	-0.0116	-0.2391	-0.0894	0.1413	0.1608	0.3452	0.1005	0.0496	0.0875	0.1206	0.0455	0.1478	-17.8349	-6.9068	-5.8743
14	0.4293	-0.6241	-1.0233	4.5209	-1.0181	4.1836	-0.0689	-0.0175	-0.0221	-0.1171	0.1289	0.1654	0.2951	-0.0448	-0.0599	0.046	-0.0028	0.0254	0.076	0.0162	0.1044	-15.3953	-3.597	-17.5584
15	1.5554	-1.3109	0.3092	3.4114	-2.0721	1.5107	0.0805	0.0733	0.0512	-0.1624	-0.0821	-0.0892	0.0922	0.0433	0.0016	0.0604	-0.0113	0.0068	0.0942	-0.008	0.0788	-17.2228	10.08	-29.0125
16	0.3022	0.7258	1.1243	7.8103	0.9615	5.224	0.1272	-0.013	-0.166	0.0373	0.3653	-0.1776	0.0779	-0.1625	-0.4925	0.3193	-0.0128	-0.1889	0.0326	0.004	0.1779	-22.4183	1.1332	-32.9642
17	2.1652	-1.5312	2.0842	6.1607	1.0942	3.3074	0.3301	-0.1519	-0.2007	-0.1141	0.2403	-0.5751	0.3647	-0.0762	-0.5704	0.1849	-0.0762	0.0097	0.0458	-0.0049	0.2201	-27.5136	-3.9729	-26.2835
18	2.5972	2.625	2.1653	2.8865	2.706	3.2426	-0.0371	0.0656	0.2037	0.016	0.113	0.1443	0.0368	-0.0152	-0.0759	0.0608	0.0181	0.0167	0.1285	0.0474	0.0819	-25.0727	9.713	-15.4625
19	3.7212	1.6385	2.8203	0.9909	0.8162	2.8194	0.0577	-0.0294	0.0675	0.0432	0.0441	0.1166	0.0144	-0.0851	-0.1018	0.0536	-0.0058	-0.0091	0.0893	-0.0139	0.0729	-22.1908	15.616	-20.3692
20	3.1795	1.0767	-4.0592	2.6443	-1.1753	5.205	0.0859	0.2814	-0.1146	0.3376	-0.2301	-0.0536	-0.0432	-0.4043	0.1442	0.1757	-0.1087	-0.07	0.1308	0.0158	0.0425	-29.9145	4.8947	-31.403

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 26
2	X-RAY DIFFRACTION	2	ALL	AAA	27 - 33
3	X-RAY DIFFRACTION	3	ALL	AAA	34 - 37
4	X-RAY DIFFRACTION	4	ALL	AAA	38 - 60
5	X-RAY DIFFRACTION	5	ALL	AAA	61 - 83
6	X-RAY DIFFRACTION	6	ALL	AAA	84 - 90
7	X-RAY DIFFRACTION	7	ALL	AAA	91 - 99
8	X-RAY DIFFRACTION	8	ALL	AAA	100 - 111
9	X-RAY DIFFRACTION	9	ALL	AAA	112 - 128
10	X-RAY DIFFRACTION	10	ALL	AAA	129 - 137
11	X-RAY DIFFRACTION	11	ALL	BBB	1 - 30
12	X-RAY DIFFRACTION	12	ALL	BBB	31 - 39
13	X-RAY DIFFRACTION	13	ALL	BBB	40 - 50
14	X-RAY DIFFRACTION	14	ALL	BBB	51 - 60
15	X-RAY DIFFRACTION	15	ALL	BBB	61 - 77
16	X-RAY DIFFRACTION	16	ALL	BBB	78 - 86
17	X-RAY DIFFRACTION	17	ALL	BBB	87 - 94
18	X-RAY DIFFRACTION	18	ALL	BBB	95 - 111
19	X-RAY DIFFRACTION	19	ALL	BBB	112 - 128
20	X-RAY DIFFRACTION	20	ALL	BBB	129 - 137

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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

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 132 molecules

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 132 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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 132 molecules

-
Details

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Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi