PDB-4y0u: Crystal Structure of 6Alpha-Hydroxymethylpenicillanate Complexed ...

ID or keywords:

Entry

Database: PDB / ID: 4y0u

Title

Crystal Structure of 6Alpha-Hydroxymethylpenicillanate Complexed with OXA-58, a Carbapenem hydrolyzing Class D betalactamase from Acinetobacter baumanii.

Components

Beta-lactamase

Keywords

HYDROLASE / ACYL-ENZYME COMPLEX / OXA-58 / 6Alpha-Hydroxymethylpenicillanate

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.6 Å

Authors

Pratap, S. / Katiki, M. / Gill, P. / Golemi-Kotra, D. / Kumar, P.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2015
Title: Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.
Authors: Pratap, S. / Katiki, M. / Gill, P. / Kumar, P. / Golemi-Kotra, D.

History

Deposition	Feb 6, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/4y0u ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y0u	HTTPS FTP

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Related structure data

Related structure data	4y0oC 4y0tC C: citing same article (ref.)
Similar structure data	4oh0-d 5jo9-d 1kku-d 4y0o-d 4y0t-2 5qaw-3 4y0t-3 5kzh-3 4y0t-1 6nz8-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) 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

Related structure data

4y0oC

4y0tC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

4

D: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	36.943, 65.659, 191.594
Angle α, β, γ (deg.)	90.00, 91.70, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 31498.209 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bla-OXA-58, bla-oxa58 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical	ChemComp-ALP / 2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID Mass: 249.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₅NO₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.84 Å³/Da / Density % sol: 33.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris base/Hydrochloric acid (pH 8.0), 30% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.6→36.93 Å / Num. obs: 21118 / % possible obs: 87.33 % / Redundancy: 3.3 % / R_merge(I) obs: 0.15 / Net I/σ(I): 8.45
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.43 / % possible all: 69.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
HKL-2000		data scaling
HKL-2000		phasing

Refinement

Resolution: 2.6→36.927 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.892 / SU B: 36.588 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26127	983	4.7 %	RANDOM
R_work	0.21928	-	-	-
obs	0.22122	20133	74.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 54.175 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.66 Å²	0 Å²	-0.41 Å²
2-	-	3.51 Å²	0 Å²
3-	-	-	-2.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→36.927 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7766	0	60	282	8108

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	8026
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	7683
X-RAY DIFFRACTION	r_angle_refined_deg	1.8	1.955	10850
X-RAY DIFFRACTION	r_angle_other_deg	1.542	3	17640
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.503	5	971
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.137	24.883	383
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.808	15	1374
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.767	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	1172
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	9099
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1897
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.602→2.67 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	58	-
R_work	0.332	1102	-
obs	-	-	55.5 %

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	13.5388	-9.0145	-11.3412	11.268	8.0208	11.3591	-0.5278	-0.836	0.0931	0.1145	0.4443	-0.3002	0.1627	1.0794	0.0834	0.1005	0.0509	0.0028	0.4647	-0.0686	0.3377	0.552	-5.156	89.167
2	11.3739	-6.0356	-3.0123	8.7421	1.6661	3.7148	0.3443	0.5644	0.1195	0.0415	-0.3384	0.0936	-0.1019	-0.0024	-0.0059	0.0864	-0.0243	-0.0905	0.3381	-0.0122	0.1776	-1.39	-0.14	79.554
3	3.6549	-0.755	0.8835	0.9103	-1.4967	3.7331	-0.1168	0.3071	0.3627	0.1883	0.0026	-0.0689	-0.412	0.2311	0.1143	0.0479	-0.0064	-0.018	0.283	0.013	0.2913	-6.279	3.462	66.904
4	0.596	-1.8115	-0.3131	10.1072	1.8294	2.9889	-0.0985	0.1203	-0.3097	0.0111	0.0238	-0.1169	0.6742	-0.0911	0.0748	0.2798	-0.0481	0.0875	0.376	-0.0555	0.5027	-16.027	-11.766	52.047
5	3.9932	1.7822	0.9616	4.3972	0.0277	3.8815	0.0244	0.3366	-0.0001	-0.2493	0.0026	-0.07	-0.1612	0.0912	-0.0269	0.0314	0.0304	-0.0078	0.3643	0.017	0.2706	-7.968	3.838	57.093
6	3.5514	-2.131	0.1198	4.729	-2.6543	6.3739	-0.0122	0.0556	-0.1376	0.1471	0.2739	0.1652	-0.3184	-0.4086	-0.2617	0.0223	0.0032	-0.0209	0.353	-0.0256	0.2678	-17.738	2.997	71.625
7	9.2894	-3.7327	-2.5262	7.4569	0.4803	3.974	-0.4517	0.6425	0.1502	0.1264	0.0381	-0.1736	0.3534	-0.3317	0.4137	0.0653	-0.0614	-0.0362	0.3555	-0.0342	0.2161	-4.914	-3.546	69.581
8	4.474	-4.612	-3.1044	9.4908	2.9197	4.5894	-0.0903	-0.7811	-0.2654	-0.2565	0.1133	0.3291	0.2212	0.3709	-0.0231	0.1423	-0.0015	-0.1542	0.4112	0.0247	0.3183	-4.3	-5.45	73.891
9	5.1406	0.4624	-6.7766	1.2319	-1.4677	13.2402	-0.1543	0.0836	-0.5655	0.0516	-0.0161	0.0969	0.286	-0.0693	0.1705	0.0702	0.0142	-0.0943	0.3874	0.0069	0.332	-8.689	-8.605	81.619
10	7.7929	5.5053	3.7692	15.823	6.0994	12.0091	-0.3178	0.2271	-0.0593	-0.4448	0.3354	0.0701	-0.229	0.1245	-0.0175	0.1414	0.0138	0.0078	0.3221	-0.026	0.3483	-15.496	34.337	55.992
11	10.7081	4.6884	-0.7852	3.963	-0.4522	1.3255	-0.1693	0.3333	-0.7536	-0.4795	0.0464	-0.6393	-0.0158	0.0881	0.1229	0.1066	0.0155	0.0248	0.3339	-0.0222	0.2681	-16.781	28.325	65.474
12	10.3657	0.8912	-4.6232	0.9363	0.2295	3.4372	0.0807	0.1216	-0.234	0.0002	-0.1216	-0.1475	-0.1586	-0.0355	0.0409	0.0279	0.0007	-0.0499	0.3338	0.0678	0.2277	-24.279	28.278	82.659
13	3.9166	-0.5811	0.2768	6.5514	-1.2037	1.8592	0.0332	0.1	0.5562	0.2204	0.0897	-0.1462	-0.3666	0.2064	-0.123	0.0893	-0.0289	-0.0203	0.3775	-0.0024	0.3279	-31.664	41.654	90.176
14	3.8542	-1.1263	-2.2521	0.5988	1.9201	7.6735	-0.1118	-0.4476	-0.2864	0.1343	0.0838	0.0325	0.8054	0.1931	0.028	0.2283	0.0343	-0.0033	0.2868	0.0223	0.3073	-24.593	22.169	90.47
15	5.6396	0.6487	0.1832	1.2013	0.103	5.3147	0.1225	0.1723	-0.224	0.2084	-0.0663	-0.1511	0.4191	0.1948	-0.0563	0.0708	0.0053	-0.0608	0.1961	0.0188	0.258	-24.966	25.317	82.326
16	1.5101	1.3345	1.0205	6.8196	-5.4177	7.8466	-0.1646	-0.0505	0.0637	-0.048	0.7542	0.5544	-0.2456	-1.0743	-0.5896	0.0423	0.1207	-0.0241	0.5912	0.0042	0.3521	-35.881	33.587	71.432
17	8.0628	2.2478	0.5911	4.078	-0.1727	4.0871	-0.5045	-0.0604	0.2516	-0.0314	0.1466	-0.0665	-0.5591	-0.0268	0.358	0.1085	0.0294	-0.0259	0.2275	-0.0003	0.2298	-20.617	35.08	75.77
18	0.5333	-0.5816	1.3187	4.528	-0.4823	6.2955	-0.0247	0.2951	0.1613	-0.3361	-0.1261	0.0923	-0.3759	-0.0069	0.1508	0.0559	0.0148	0.0158	0.5263	0.0168	0.3319	-23.181	36.999	66.326
19	5.5876	0.5012	2.246	0.8151	-0.1159	5.6651	0.0388	0.3128	0.0255	-0.1893	0.0753	0.104	-0.1783	-0.2762	-0.1141	0.0685	0.038	-0.0247	0.2173	-0.0052	0.3332	-38.749	29.431	25.064
20	1.4996	-3.8325	0.4223	10.0037	-0.2788	6.9399	0.1468	0.0111	-0.5749	-0.3343	-0.1004	1.2712	0.9613	-0.0321	-0.0463	0.251	-0.0025	-0.0178	0.5856	0.097	0.7599	-26.676	15.211	46.031
21	3.4175	-1.601	1.3949	1.9766	0.183	3.7754	-0.1404	-0.3376	-0.0698	0.2557	0.0043	0.1121	-0.2022	-0.1613	0.1362	0.0648	-0.0098	-0.0117	0.3879	0.0156	0.2961	-34.481	30.631	42.254
22	4.3614	0.5086	-0.4569	4.4623	4.188	5.956	0.016	0.0578	-0.0914	-0.2869	0.0511	-0.3048	-0.47	0.3968	-0.0672	0.0453	-0.0279	-0.0309	0.3368	0.1151	0.243	-24.916	31.391	27.648
23	8.1217	0.6968	-5.5833	6.3492	-2.3808	7.119	-0.5426	-0.1921	-0.0424	-0.2048	0.352	0.1182	0.9441	-0.0219	0.1907	0.202	-0.0276	-0.0699	0.3037	-0.0006	0.2178	-38.147	24.222	29.508
24	3.1056	3.691	-1.3902	11.8751	-2.3622	3.0776	-0.336	0.5236	-0.6512	-0.165	0.0182	-0.2186	0.286	-0.1665	0.3178	0.2142	-0.0153	-0.0263	0.4163	-0.063	0.3408	-37.55	23.622	24.168
25	4.235	1.4057	-5.5589	1.8985	-0.0853	9.5825	-0.5193	0.0793	-0.3163	-0.1157	0.2535	-0.0573	0.818	0.1053	0.2658	0.123	0.051	-0.1017	0.4468	0.0043	0.4583	-33.751	20.204	16.926
26	4.8137	-0.832	0.2629	2.2359	-2.7922	4.3054	0.0029	-0.6847	0.4089	0.1371	0.209	0.2442	0.1404	-0.4099	-0.2119	0.1773	-0.074	0.0329	0.6552	-0.0945	0.5024	-59.129	53.97	28.437
27	3.6026	0.1499	-0.7385	1.4995	-0.2592	3.0346	-0.0195	-0.0245	0.4375	-0.0158	-0.0167	-0.0466	-0.1119	0.0464	0.0363	0.0153	0.0293	-0.0554	0.3654	-0.0215	0.3907	-46.27	58.973	9.92
28	2.2326	0.6717	1.8228	4.5382	-1.6239	9.006	-0.0157	-0.583	0.7039	0.2409	0.1758	-0.1213	-0.212	-0.0594	-0.1601	0.111	-0.0082	0.06	0.4902	-0.1609	0.5764	-51.696	61.079	27.584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	38 - 49
2	X-RAY DIFFRACTION	2	A	50 - 64
3	X-RAY DIFFRACTION	3	A	65 - 101
4	X-RAY DIFFRACTION	4	A	102 - 121
5	X-RAY DIFFRACTION	5	A	122 - 181
6	X-RAY DIFFRACTION	6	A	182 - 221
7	X-RAY DIFFRACTION	7	A	222 - 241
8	X-RAY DIFFRACTION	8	A	242 - 261
9	X-RAY DIFFRACTION	9	A	262 - 280
10	X-RAY DIFFRACTION	10	B	38 - 50
11	X-RAY DIFFRACTION	11	B	51 - 71
12	X-RAY DIFFRACTION	12	B	72 - 100
13	X-RAY DIFFRACTION	13	B	101 - 140
14	X-RAY DIFFRACTION	14	B	141 - 160
15	X-RAY DIFFRACTION	15	B	161 - 200
16	X-RAY DIFFRACTION	16	B	201 - 220
17	X-RAY DIFFRACTION	17	B	221 - 240
18	X-RAY DIFFRACTION	18	B	241 - 280
19	X-RAY DIFFRACTION	19	C	39 - 100
20	X-RAY DIFFRACTION	20	C	101 - 120
21	X-RAY DIFFRACTION	21	C	121 - 180
22	X-RAY DIFFRACTION	22	C	181 - 220
23	X-RAY DIFFRACTION	23	C	221 - 240
24	X-RAY DIFFRACTION	24	C	241 - 260
25	X-RAY DIFFRACTION	25	C	261 - 280
26	X-RAY DIFFRACTION	26	D	37 - 81
27	X-RAY DIFFRACTION	27	D	82 - 240
28	X-RAY DIFFRACTION	28	D	241 - 279

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-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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Validation report

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Links

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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

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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