PDB-4glo: Crystal structure of a short chain dehydrogenase homolog (target ...

ID or keywords:

Entry

Database: PDB / ID: 4glo

Title

Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NAD

Components

3-oxoacyl-[acyl-carrier protein] reductase

Keywords

OXIDOREDUCTASE / putative sugar dehydrogenase / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

L-fucose dehydrogenase / fucose catabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Burkholderia multivorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Vetting, M.W. / Hobbs, M.E. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

Citation

Journal: To be Published
Title: Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NAD
Authors: Vetting, M.W. / Hobbs, M.E. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

History

Deposition	Aug 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4glo.cif.gz	408.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4glo.ent.gz	336.2 KB	Display	PDB format
PDBx/mmJSON format	4glo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4glo_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	4glo_full_validation.pdf.gz	2.5 MB	Display
Data in XML	4glo_validation.xml.gz	48.9 KB	Display
Data in CIF	4glo_validation.cif.gz	70.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/4glo ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4glo	HTTPS FTP

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Related structure data

Related structure data	4gkbS S: Starting model for refinement
Similar structure data	4gkb-d 4gvx-2 6qhe-1 1g6k-1 3rwt-1 3tox-3 4gvx-1 4ure-1 3aus-1 6ds1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-505321

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (2) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: 3-oxoacyl-[acyl-carrier protein] reductase

B: 3-oxoacyl-[acyl-carrier protein] reductase

C: 3-oxoacyl-[acyl-carrier protein] reductase

D: 3-oxoacyl-[acyl-carrier protein] reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.590, 99.590, 206.389
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	3-oxoacyl-[acyl-carrier protein] reductase / Short-chain dehydrogenase/reductase SDR Mass: 27710.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / Gene: fabG, Bmul_3598, BMULJ_04919 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) References: UniProt: A9ANE0, UniProt: A0A0H3KNE7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase

#1: Protein

3-oxoacyl-[acyl-carrier protein] reductase / Short-chain dehydrogenase/reductase SDR

Mass: 27710.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / Gene: fabG, Bmul_3598, BMULJ_04919 / Plasmid: pET30 / Production host:

Escherichia coli (E. coli)
References: UniProt: A9ANE0, UniProt: A0A0H3KNE7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase

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Non-polymers , 5 types, 891 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 866 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.86 %
Crystal grow	Temperature: 298 K / pH: 7.5 Details: Protein (50 mM Hepes pH 7.5; Reservoir (100 mM MES pH 6.0, 1.3 M AmSO4); Cryoprotection (Reservoir, + 20% Ethylene glycol + 5 mM NAD), sitting drop vapor diffusion, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2012 / Details: MIRRORS
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.8→86.247 Å / Num. obs: 106861 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / R_merge(I) obs: 0.131 / R_sym value: 0.131 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 11 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 1 / R_sym value: 0.81 / % possible all: 100

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GKB

4gkb

Resolution: 1.8→28.75 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.15 / σ(F): 0 / Phase error: 17.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.181	5323	4.99 %
R_work	0.15	-	-
obs	0.152	106756	100 %
all	-	106756	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 18.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→28.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7641	0	257	866	8764

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8176
X-RAY DIFFRACTION	f_angle_d	1.522	11169
X-RAY DIFFRACTION	f_dihedral_angle_d	14.781	2883
X-RAY DIFFRACTION	f_chiral_restr	0.144	1284
X-RAY DIFFRACTION	f_plane_restr	0.005	1426

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 (%)
1.8-1.8204	0.2478	188	0.2088	3363	X-RAY DIFFRACTION	100
1.8204-1.8419	0.2479	182	0.1979	3386	X-RAY DIFFRACTION	100
1.8419-1.8643	0.2248	170	0.1888	3343	X-RAY DIFFRACTION	100
1.8643-1.8879	0.2074	180	0.1823	3378	X-RAY DIFFRACTION	100
1.8879-1.9127	0.2067	177	0.1876	3423	X-RAY DIFFRACTION	100
1.9127-1.9389	0.2058	177	0.1811	3346	X-RAY DIFFRACTION	100
1.9389-1.9666	0.2107	188	0.1701	3356	X-RAY DIFFRACTION	100
1.9666-1.996	0.2137	162	0.1719	3414	X-RAY DIFFRACTION	100
1.996-2.0272	0.2034	164	0.1619	3398	X-RAY DIFFRACTION	100
2.0272-2.0604	0.1936	181	0.1611	3322	X-RAY DIFFRACTION	100
2.0604-2.0959	0.184	193	0.1581	3347	X-RAY DIFFRACTION	100
2.0959-2.134	0.1848	160	0.1418	3421	X-RAY DIFFRACTION	100
2.134-2.175	0.2027	178	0.1448	3383	X-RAY DIFFRACTION	100
2.175-2.2194	0.168	178	0.1424	3373	X-RAY DIFFRACTION	100
2.2194-2.2677	0.1733	147	0.1501	3421	X-RAY DIFFRACTION	100
2.2677-2.3204	0.1847	179	0.1436	3376	X-RAY DIFFRACTION	100
2.3204-2.3784	0.1944	164	0.1373	3385	X-RAY DIFFRACTION	100
2.3784-2.4427	0.1641	172	0.1427	3387	X-RAY DIFFRACTION	100
2.4427-2.5145	0.1834	155	0.1464	3389	X-RAY DIFFRACTION	100
2.5145-2.5956	0.1673	177	0.1482	3365	X-RAY DIFFRACTION	100
2.5956-2.6883	0.1739	164	0.1511	3430	X-RAY DIFFRACTION	100
2.6883-2.7959	0.2058	159	0.1451	3381	X-RAY DIFFRACTION	100
2.7959-2.923	0.1788	197	0.1529	3377	X-RAY DIFFRACTION	100
2.923-3.0769	0.1671	173	0.1484	3373	X-RAY DIFFRACTION	100
3.0769-3.2695	0.1769	194	0.1467	3376	X-RAY DIFFRACTION	100
3.2695-3.5215	0.1639	176	0.1416	3396	X-RAY DIFFRACTION	100
3.5215-3.8751	0.1667	200	0.1353	3355	X-RAY DIFFRACTION	100
3.8751-4.4341	0.1644	191	0.1258	3370	X-RAY DIFFRACTION	100
4.4341-5.5798	0.1652	196	0.1379	3406	X-RAY DIFFRACTION	100
5.5798-28.7527	0.1897	201	0.1719	3393	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	1.6882	-0.2641	-0.2245	1.9492	-0.6724	0.9631	0.0219	0.1987	0.1159	-0.3978	-0.0381	-0.2956	-0.1537	0.2123	-0.0086	0.1148	-0.0429	0.0424	0.1577	0.0318	0.098	118.4642	-23.6635	-23.5739
2	0.5669	-0.004	0.2083	1.0302	0.0523	0.8257	-0.0258	0.1188	0.0705	-0.1722	0.0035	-0.0505	-0.1345	0.106	0.015	0.0706	-0.0281	-0.0029	0.0899	0.0212	0.0505	110.8357	-19.5031	-12.9499
3	1.0923	-0.2825	0.8847	0.7138	0.2337	2.1407	-0.1282	0.0305	0.3428	-0.053	0.1338	-0.095	-0.6984	0.4135	0.1186	0.2255	-0.1714	0.0093	0.1925	-0.0886	0.1203	119.753	-25.3884	-8.5563
4	3.4093	1.4424	1.6401	2.5198	1.2851	3.5747	0.16	-0.4941	0.246	0.2202	-0.0147	-0.2769	-0.3165	0.3569	-0.0449	0.0714	-0.0808	0.0285	0.3003	-0.0772	0.1921	132.8081	-30.9391	-1.0964
5	0.7323	-0.0277	0.1686	0.5519	-0.0387	0.6002	-0.0021	0.066	-0.0432	-0.0715	0.0101	-0.1017	0.0382	0.1425	0.0021	0.0465	-0.0108	0.0171	0.0895	-0.0089	0.0649	117.4077	-36.2129	-10.9641
6	1.2854	0.4862	-0.5345	2.3512	-0.0213	1.9935	0.0138	-0.1183	-0.0173	0.3159	-0.0882	0.3427	-0.0514	-0.2316	0.0275	0.0882	-0.0234	0.0351	0.124	-0.0231	0.0649	93.9296	-28.4614	22.5834
7	0.4989	-0.0458	0.1298	0.8881	0.0406	1.074	-0.0272	-0.0779	0.0518	0.1326	-0.0155	0.0772	-0.0779	-0.094	0.0415	0.0504	-0.0104	-0.0057	0.069	-0.0072	0.0548	100.0382	-22.1899	12.0546
8	1.3782	0.1947	0.9922	0.4989	0.1081	1.3721	-0.2113	-0.1841	0.3505	-0.0753	-0.1084	0.3438	-0.4543	-0.6758	0.1991	0.1327	0.1019	-0.053	0.3453	-0.0382	0.2045	88.8678	-32.1857	5.805
9	3.5188	-2.0564	1.5889	3.541	-0.1916	3.7509	-0.0393	0.3114	-0.2133	-0.3687	-0.034	0.3948	-0.0966	-0.5113	0.0367	0.1064	-0.0602	-0.0149	0.2293	0.0046	0.1567	84.1325	-42.2977	0.6293
10	0.7516	0.1404	0.1996	0.6118	0.2956	0.8193	-0.0359	-0.0551	-0.0851	0.0372	-0.0107	0.0345	0.0696	-0.0618	0.0399	0.0778	-0.0305	0.0104	0.0641	0.0177	0.064	100.4409	-39.7753	10.3987
11	0.3673	-0.1237	-0.0616	1.1275	0.041	0.1842	-0.0268	-0.1658	-0.1362	0.2065	-0.0195	0.1827	0.1195	-0.018	0.005	0.2647	-0.0646	0.0938	0.0944	0.1098	0.1649	99.1085	-54.656	23.4225
12	1.2636	0.3742	-0.4899	2.4533	-0.0584	2.2799	-0.0286	-0.2616	-0.1773	0.3311	-0.0347	-0.0524	0.2426	0.1558	0.0378	0.2791	-0.0448	-0.0213	0.1309	0.1533	0.1647	107.1303	-57.8724	25.4812
13	0.4765	0.1386	-0.2853	0.5797	0.1479	0.9967	-0.0607	-0.3313	-0.4836	0.2979	0.053	-0.1547	0.5317	0.458	0.1401	0.2871	-0.0083	0.0745	-0.0081	0.183	0.2482	108.4498	-64.5102	15.416
14	3.6187	1.8882	-2.2736	1.9583	-0.5425	2.5131	-0.002	0.0919	0.1069	0.1204	0.0828	-0.0453	0.1079	0.0842	-0.0594	0.0724	-0.0047	-0.0069	0.0603	0.0436	0.0922	112.4112	-51.6632	8.4587
15	1.5991	0.3251	-0.6431	2.3942	0.2938	1.2429	-0.0071	-0.2839	-0.351	0.1876	-0.0608	-0.1545	0.2704	0.0932	0.0334	0.125	-0.0054	0.03	0.046	0.0659	0.0905	109.0193	-53.1887	8.9203
16	3.289	1.3946	-0.5844	1.4829	-0.1879	3.7049	-0.0903	-0.1906	-0.5706	0.14	-0.0227	-0.6488	0.1986	0.6399	0.0245	0.0961	0.006	-0.047	0.1946	0.0246	0.2166	124.6709	-39.8975	18.0235
17	0.9252	0.2639	0.0192	0.6487	0.0786	0.4929	0.0199	-0.0994	-0.0667	0.1423	0.0014	0.0082	0.084	0.0369	-0.0163	0.0979	-0.0177	0.0062	0.0699	0.0231	0.0582	107.4113	-43.4282	13.6113
18	1.0829	-0.886	0.0191	1.6119	0.7217	1.2493	-0.0237	0.1921	-0.1292	-0.3666	-0.0286	-0.2548	0.1359	0.0733	0.0719	0.1475	0.0103	0.0739	0.151	-0.052	0.149	121.4184	-53.5445	-24.7218
19	0.5117	-0.1168	-0.066	0.8752	0.1834	0.7855	-0.0756	0.0538	-0.2129	-0.0635	0.0289	-0.1484	0.2079	0.1158	0.0411	0.1268	0.0144	0.0453	0.0825	-0.0242	0.1661	119.6679	-58.2591	-12.1122
20	2.3987	0.1506	0.1263	3.8437	1.4627	2.7769	-0.1988	0.6982	-0.7698	-0.4601	-0.0486	0.622	0.5311	-0.4648	0.1055	0.2863	-0.1525	0.0193	0.3135	-0.227	0.423	95.8329	-54.2232	-19.9763
21	1.3094	-0.419	-0.2853	0.5873	-0.0281	0.8552	-0.0199	0.1569	-0.145	-0.1136	-0.0155	-0.0105	0.0302	-0.0416	0.0215	0.0712	-0.0183	0.0082	0.058	-0.0205	0.0601	109.6441	-43.1081	-14.9988

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 170 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 171 through 200 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 201 through 220 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 221 through 258 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 43 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 44 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 175 through 200 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 220 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 221 through 258 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 17 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 18 through 43 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 44 through 131 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 132 through 150 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 151 through 203 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 204 through 220 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 221 through 258 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 43 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 44 through 183 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 184 through 211 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 212 through 258 )

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Protein , 1 types, 4 molecules ABCD

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 891 molecules

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+About Yorodumi

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

-Aug 12, 2020. Covid-19 info

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+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 , 5 types, 891 molecules

-
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