PDB-4hxg: Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic cryst...

ID or keywords:

Entry

Database: PDB / ID: 4hxg

Title

Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic crystal form)

Components

Putative uncharacterized protein PH0594

Keywords

HYDROLASE / self-compartmentalization /

beta-propeller / alpha/beta hyrdolase fold

Function / homology

Function and homology information

serine-type peptidase activity /

proteolysis /

metal ion binding
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Kiss-Szeman, A. / Menyhard, D.K. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION.
Authors: Menyhard, D.K. / Kiss-Szeman, A. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V.

History

Deposition	Nov 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2013	Group: Database references
Revision 1.2	Jul 3, 2013	Group: Database references
Revision 1.3	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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Download

PDBx/mmCIF format	4hxg.cif.gz	2.7 MB	Display	PDBx/mmCIF format
PDB format	pdb4hxg.ent.gz	2.3 MB	Display	PDB format
PDBx/mmJSON format	4hxg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/4hxg ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hxg	HTTPS FTP

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Related structure data

Related structure data	4hxeC 4hxfSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4hxf-1 4hxe-1 3upf-4 3ur0-4 4nru-7 6vcf-d 3uqs-4 1mx9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #225 - Sep 2018 Phytase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Putative uncharacterized protein PH0594

B: Putative uncharacterized protein PH0594

C: Putative uncharacterized protein PH0594

D: Putative uncharacterized protein PH0594

E: Putative uncharacterized protein PH0594

F: Putative uncharacterized protein PH0594

G: Putative uncharacterized protein PH0594

H: Putative uncharacterized protein PH0594

I: Putative uncharacterized protein PH0594

J: Putative uncharacterized protein PH0594

K: Putative uncharacterized protein PH0594

L: Putative uncharacterized protein PH0594

hetero molecules

883 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein PH0594

B: Putative uncharacterized protein PH0594

C: Putative uncharacterized protein PH0594

D: Putative uncharacterized protein PH0594

E: Putative uncharacterized protein PH0594

F: Putative uncharacterized protein PH0594

hetero molecules

defined by author&software
443 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Putative uncharacterized protein PH0594

H: Putative uncharacterized protein PH0594

I: Putative uncharacterized protein PH0594

J: Putative uncharacterized protein PH0594

K: Putative uncharacterized protein PH0594

L: Putative uncharacterized protein PH0594

hetero molecules

defined by author&software
441 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.310, 183.800, 275.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative uncharacterized protein PH0594 Mass: 73320.281 Da / Num. of mol.: 12 / Mutation: S466A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0594 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O58323, acylaminoacyl-peptidase
#2: Chemical	... ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol Mass: 118.174 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₆H₁₄O₂
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1147 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.4 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0715 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2006 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0715 Å / Relative weight: 1
Reflection	Resolution: 2.65→20 Å / Num. all: 255208 / Num. obs: 255208 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.39 % / B_iso Wilson estimate: 50.89 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 16.47
Reflection shell	Resolution: 2.65→2.72 Å / Redundancy: 4.335 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 2.36 / Num. unique all: 19084 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HXF

4hxf

Resolution: 2.7→19.98 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.85 / Stereochemistry target values: ML / Details: Ramachandran restraints were applied

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2407	1751	0.79 %	thin shells
R_work	0.1999	-	-	-
all	0.2002	222127	-	-
obs	0.2002	222127	87.59 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.004 Å² / k_sol: 0.276 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.7705 Å²	-0 Å²	-0 Å²
2-	-	-8.7263 Å²	-0 Å²
3-	-	-	-21.1662 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	58377	0	231	1147	59755

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	60324
X-RAY DIFFRACTION	f_angle_d	0.979	81727
X-RAY DIFFRACTION	f_dihedral_angle_d	14.136	21378
X-RAY DIFFRACTION	f_chiral_restr	0.077	8515
X-RAY DIFFRACTION	f_plane_restr	0.005	10492

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 (%)
2.7-2.7728	0.3845	143	0.3393	14464	X-RAY DIFFRACTION	76
2.7728-2.8542	0.3787	74	0.3227	15080	X-RAY DIFFRACTION	78
2.8542-2.946	0.3724	154	0.3043	15350	X-RAY DIFFRACTION	80
2.946-3.051	0.2931	86	0.2674	16076	X-RAY DIFFRACTION	83
3.051-3.1727	0.2871	181	0.2349	16648	X-RAY DIFFRACTION	87
3.1727-3.3165	0.2572	86	0.2235	17115	X-RAY DIFFRACTION	89
3.3165-3.4904	0.2551	183	0.2138	17458	X-RAY DIFFRACTION	91
3.4904-3.7078	0.2452	92	0.2101	17761	X-RAY DIFFRACTION	92
3.7078-3.992	0.2589	190	0.1901	17905	X-RAY DIFFRACTION	92
3.992-4.3899	0.1964	91	0.1588	18048	X-RAY DIFFRACTION	93
4.3899-5.0163	0.1675	192	0.1368	18119	X-RAY DIFFRACTION	93
5.0163-6.2872	0.2384	94	0.1752	18159	X-RAY DIFFRACTION	93
6.2872-19.9807	0.2015	185	0.1718	18193	X-RAY DIFFRACTION	91

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	0.0244	-0.0257	-0.0501	0.014	0.0235	0.0798	-0.1266	0.0308	-0.1833	-0.0305	0.0233	-0.018	0.2125	0.0955	-0.065	0.3557	0.0181	0.1207	0.3075	-0.0959	0.3957	66.8984	-13.189	-32.1439
2	0.0397	-0.0027	0.0035	0.0686	-0.0129	0.0231	-0.0737	0.2249	-0.0493	-0.2498	-0.0487	-0.0197	0.0318	0.0297	-0.1609	-0.0246	-0.103	0.0003	0.098	-0.3364	-0.4382	58.8604	12.4611	-45.6647
3	0.0199	0.0094	-0.0059	0.0084	0.005	0.0283	-0.0896	0.0814	-0.1279	-0.0344	-0.0096	0.0024	0.171	-0.1386	-0.1033	0.4629	-0.1766	0.0928	0.3373	-0.1336	0.4808	20.7687	-21.0762	-21.0321
4	0.0484	0.0236	-0.0308	0.0203	0.0037	0.0445	-0.0872	0.0272	-0.1435	0.0331	-0.0484	0.0763	0.183	-0.1756	-0.1442	0.3938	-0.2062	0.123	0.3849	-0.0808	0.4299	2.7328	-18.0746	2.8106
5	0.0052	-0.0065	-0.0018	0.0141	0.0107	0.0186	-0.0267	-0.033	-0.181	-0.0346	-0.0236	0.0004	0.2683	0.0629	0.0076	0.5959	0.1267	0.1892	0.1929	0.0867	0.5623	55.4937	-37.1936	7.9718
6	0.0259	-0.017	0.0318	0.0132	-0.0139	0.0315	-0.0306	-0.0715	-0.1033	0.0479	-0.021	-0.1727	0.212	0.1131	-0.0124	0.5331	0.3436	0.1251	0.568	0.213	0.6333	80.3449	-26.504	21.0682
7	0.0334	-0.0127	-0.0188	0.0059	-0.0108	0.0161	-0.0083	0.0053	0.006	0.0076	-0.0225	0.0305	-0.0351	0.0176	-0.0366	0.0974	-0.0271	-0.004	0.1655	-0.0021	0.1511	56.6612	39.6913	-7.2414
8	0.0175	0.0173	-0.0208	0.0263	-0.0059	0.0148	-0.0024	0.0061	-0.0172	-0.0397	0.0009	-0.0952	-0.0338	0.1155	0.0008	0.1586	-0.0646	0.007	0.3189	-0.0072	0.271	83.0272	28.7535	-16.9945
9	0.012	-0.0025	-0.0168	0.0073	0.0068	0.0649	-0.0277	-0.1175	0.0079	0.0408	0.0382	-0.0145	0.0308	-0.067	0.0074	0.1797	0.055	0.0032	0.3073	0.0066	0.2832	18.8718	24.0266	17.6477
10	0.062	-0.0059	0.0116	0.0064	0.0212	0.0254	-0.0395	-0.0018	0.0345	-0.0247	-0.0023	0.0949	-0.0151	-0.2439	-0.087	0.1372	0.0269	-0.031	0.3875	-0.0238	0.2765	3.7306	21.1601	-8.381
11	0.0241	0.0335	-0.0178	0.0148	-0.0222	0.0437	-0.0241	-0.1563	-0.0338	0.029	-0.074	-0.0537	0.0077	0.1777	-0.0845	0.1483	0.0084	-0.0284	0.3807	0.0731	0.2157	63.2226	15.7244	33.856
12	0.0214	0.0122	0.0183	0.0641	0.0359	0.0475	-0.0619	-0.2157	0.0085	0.175	-0.1865	0.008	0.104	0.0199	-0.0915	0.2039	0.1569	-0.0316	0.2767	0.3153	0.0904	53.1793	-9.6912	46.5829
13	0.0402	0.022	-0.0444	0.0647	0.0036	0.1353	-0.0625	0.012	-0.0574	-0.0706	-0.0686	0.0154	0.1276	0.0743	-0.1314	0.6432	0.0436	0.0616	0.3143	-0.0124	0.2216	121.7459	-17.2731	34.3139
14	0.0981	0.0184	0.0336	0.0531	-0.0259	0.1189	-0.0609	0.0818	-0.0187	-0.1472	-0.0739	-0.0571	-0.0844	0.1384	-0.0246	0.5833	0.0893	0.1059	0.6505	0.0743	0.2914	147.0101	-7.2071	21.694
15	-0.004	-0.0141	0.0089	0.0509	-0.0599	0.0699	0.0095	0.0429	0.0373	0.0881	-0.0115	0.0023	-0.1832	0.0631	0.0246	0.8306	-0.0074	0.0075	0.2466	0.0268	0.2747	113.3939	26.7585	51.5068
16	0.0028	0.0031	0.0162	0.0424	0.0142	0.0271	0.0138	-0.0612	0.0557	0.1493	-0.0152	0.0106	-0.1953	0.0143	0.0176	1.2329	-0.0981	-0.0722	0.1353	-0.0644	0.2581	116.5471	41.352	77.4116
17	0.0136	0.0126	-0.0045	0.0397	0.0009	0.0211	0.0173	-0.0346	0.0012	0.1165	-0.0302	0.0578	0.0123	-0.0357	-0.0047	0.6758	-0.0136	0.0457	0.3327	-0.0211	0.3321	97.9796	-11.5128	75.6908
18	0.0136	0.0023	0.0005	0.0367	-0.0277	0.0229	0.0207	-0.0541	-0.0451	0.1105	-0.0079	0.0503	0.1404	-0.027	0.0145	0.8299	-0.0289	0.0455	0.2111	-0.0007	0.2544	109.0762	-37.8099	85.3511
19	0.0402	-0.0115	0.0595	0.0422	-0.0063	0.1113	-0.0109	0.0831	0.0345	-0.0003	0.0047	-0.1548	0.0062	0.2011	0.08	0.3435	0.0548	-0.0596	0.994	0.2858	0.4073	174.2594	-10.1292	60.2677
20	0.0263	0.0007	0.0069	0.034	0.0365	0.0331	0.057	0.0847	-0.0519	-0.0113	-0.0023	-0.0937	0.082	0.1405	0.0147	0.7422	0.3929	0.1153	0.7967	0.152	0.4944	163.7937	-34.5056	46.5798
21	0.0428	0.0178	0.0241	0.0037	0.0107	0.0118	-0.0311	-0.0106	0.0014	0.0726	-0.0533	-0.1225	-0.1841	0.1266	-0.0296	0.9141	-0.4558	-0.3692	0.7168	0.1825	0.4966	158.2336	24.1616	89.6227
22	0.0051	0.015	0.0059	0.0315	-0.0065	0.0103	0.0004	0.0226	0.0777	0.0585	-0.0369	-0.0969	-0.1111	0.0874	0.0093	1.0008	-0.5836	-0.2775	0.5098	0.2197	0.56	155.4129	42.3302	66.0871
23	0.0382	-0.0101	-0.0086	0.0061	-0.0025	0.0212	-0.0461	-0.0004	-0.0123	-0.0147	-0.069	-0.0565	0.1291	0.2016	-0.0782	0.7506	0.0469	-0.1362	0.8132	0.2037	0.4787	151.0265	-21.8975	100.2318
24	0.1565	0.0421	-0.0264	0.0604	-0.008	0.0171	-0.0741	-0.2502	-0.0121	0.12	-0.0743	-0.073	0.0874	0.1116	0.0145	0.6442	-0.0623	-0.0736	0.4204	0.0387	0.0768	125.4053	-14.0332	114.0552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 4:340)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 350:618)
3	X-RAY DIFFRACTION	3	chain 'B' and (resseq 4:340)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 350:618)
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 4:340)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 350:618)
7	X-RAY DIFFRACTION	7	chain 'D' and (resseq 4:340)
8	X-RAY DIFFRACTION	8	chain 'D' and (resseq 350:618)
9	X-RAY DIFFRACTION	9	chain 'E' and (resseq 4:340)
10	X-RAY DIFFRACTION	10	chain 'E' and (resseq 350:618)
11	X-RAY DIFFRACTION	11	chain 'F' and (resseq 4:340)
12	X-RAY DIFFRACTION	12	chain 'F' and (resseq 350:618)
13	X-RAY DIFFRACTION	13	chain 'G' and (resseq 4:340)
14	X-RAY DIFFRACTION	14	chain 'G' and (resseq 350:618)
15	X-RAY DIFFRACTION	15	chain 'H' and (resseq 4:340)
16	X-RAY DIFFRACTION	16	chain 'H' and (resseq 350:618)
17	X-RAY DIFFRACTION	17	chain 'I' and (resseq 4:340)
18	X-RAY DIFFRACTION	18	chain 'I' and (resseq 350:618)
19	X-RAY DIFFRACTION	19	chain 'J' and (resseq 4:340)
20	X-RAY DIFFRACTION	20	chain 'J' and (resseq 350:618)
21	X-RAY DIFFRACTION	21	chain 'K' and (resseq 4:340)
22	X-RAY DIFFRACTION	22	chain 'K' and (resseq 350:618)
23	X-RAY DIFFRACTION	23	chain 'L' and (resseq 4:340)
24	X-RAY DIFFRACTION	24	chain 'L' and (resseq 350:618)

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News

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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.
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