PDB-4mo4: Crystal structure of AnmK bound to AMPPCP

ID or keywords:

Entry

Database: PDB / ID: 4mo4

Title

Crystal structure of AnmK bound to AMPPCP

Components

Anhydro-N-acetylmuramic acid kinase

Keywords

TRANSFERASE / ATPase domain / kinase / ATP-binding

Function / homology

Function and homology information

anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / response to antibiotic / ATP binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

Bacik, J.P. / Mark, B.L.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Conformational Itinerary of Pseudomonas aeruginosa 1,6-Anhydro-N-acetylmuramic Acid Kinase during Its Catalytic Cycle.
Authors: Bacik, J.P. / Tavassoli, M. / Patel, T.R. / McKenna, S.A. / Vocadlo, D.J. / Khajehpour, M. / Mark, B.L.

History

Deposition	Sep 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2014	Group: Database references
Revision 1.2	Mar 5, 2014	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 / struct_ref_seq_dif / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR DETERMINED

Remark 700

SHEET DETERMINATION METHOD: AUTHOR DETERMINED

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mo4.cif.gz	553.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4mo4.ent.gz	455.9 KB	Display	PDB format
PDBx/mmJSON format	4mo4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mo4_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4mo4_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4mo4_validation.xml.gz	59.9 KB	Display
Data in CIF	4mo4_validation.cif.gz	89.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/4mo4 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mo4	HTTPS FTP

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Related structure data

Related structure data	4mo5C 3qbwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4mo5-1 5ekd-d 4mo5-2 2hz7-d 2ol3-d 2nvw-d 1nam-d 6wio-d 2yy5-2 5vk6-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) 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	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Anhydro-N-acetylmuramic acid kinase

B: Anhydro-N-acetylmuramic acid kinase

C: Anhydro-N-acetylmuramic acid kinase

D: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

1

A: Anhydro-N-acetylmuramic acid kinase

B: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

2

C: Anhydro-N-acetylmuramic acid kinase

D: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.657, 70.823, 91.211
Angle α, β, γ (deg.)	106.50, 104.93, 98.26
Int Tables number	1
Space group name H-M	P1

#1: Protein	Anhydro-N-acetylmuramic acid kinase / AnhMurNAc kinase Mass: 40133.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I5Q5, anhydro-N-acetylmuramic acid kinase
#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1165 / 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: 2.16 Å³/Da / Density % sol: 43.11 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 9 Details: 26% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 22, 2012
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.67→44.86 Å / Num. all: 156111 / Num. obs: 151753 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / B_iso Wilson estimate: 23.584 Å² / R_merge(I) obs: 0.05 / R_sym value: 0.06 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.67→1.76 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.593 / Mean I/σ(I) obs: 2 / Num. unique all: 21751 / R_sym value: 0.712 / % possible all: 95.2

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QBW

3qbw

Resolution: 1.67→44.856 Å / SU ML: 0.18 / σ(F): 1.96 / Phase error: 23.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2133	7765	5.12 %	RANDOM
R_work	0.1769	-	-	-
obs	0.1788	151721	97.19 %	-
all	-	151753	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.67→44.856 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10417	0	120	1165	11702

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10803
X-RAY DIFFRACTION	f_angle_d	1.16	14760
X-RAY DIFFRACTION	f_dihedral_angle_d	12.631	3855
X-RAY DIFFRACTION	f_chiral_restr	0.074	1646
X-RAY DIFFRACTION	f_plane_restr	0.006	1945

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 (%)
1.67-1.689	0.313	217	0.2753	4635	X-RAY DIFFRACTION	93
1.689-1.7089	0.2859	264	0.2569	4713	X-RAY DIFFRACTION	96
1.7089-1.7297	0.2869	268	0.2446	4753	X-RAY DIFFRACTION	96
1.7297-1.7516	0.2976	280	0.2425	4714	X-RAY DIFFRACTION	96
1.7516-1.7746	0.2826	260	0.2396	4685	X-RAY DIFFRACTION	96
1.7746-1.799	0.288	254	0.2325	4757	X-RAY DIFFRACTION	96
1.799-1.8247	0.252	260	0.225	4759	X-RAY DIFFRACTION	96
1.8247-1.8519	0.2428	268	0.2157	4690	X-RAY DIFFRACTION	96
1.8519-1.8808	0.2768	250	0.2135	4790	X-RAY DIFFRACTION	97
1.8808-1.9117	0.2341	277	0.201	4773	X-RAY DIFFRACTION	97
1.9117-1.9446	0.2411	258	0.1979	4723	X-RAY DIFFRACTION	96
1.9446-1.98	0.2306	248	0.1981	4782	X-RAY DIFFRACTION	97
1.98-2.0181	0.2412	275	0.1959	4808	X-RAY DIFFRACTION	97
2.0181-2.0593	0.2342	258	0.1884	4759	X-RAY DIFFRACTION	97
2.0593-2.104	0.2492	262	0.1842	4784	X-RAY DIFFRACTION	97
2.104-2.153	0.2563	251	0.1867	4814	X-RAY DIFFRACTION	97
2.153-2.2068	0.2429	258	0.1877	4870	X-RAY DIFFRACTION	97
2.2068-2.2665	0.2216	247	0.1816	4748	X-RAY DIFFRACTION	98
2.2665-2.3332	0.2425	234	0.18	4847	X-RAY DIFFRACTION	97
2.3332-2.4085	0.2382	282	0.1797	4805	X-RAY DIFFRACTION	98
2.4085-2.4946	0.2035	263	0.179	4831	X-RAY DIFFRACTION	98
2.4946-2.5944	0.2321	254	0.177	4897	X-RAY DIFFRACTION	98
2.5944-2.7125	0.2192	266	0.1803	4823	X-RAY DIFFRACTION	98
2.7125-2.8555	0.2225	247	0.1757	4865	X-RAY DIFFRACTION	98
2.8555-3.0343	0.2226	235	0.1849	4872	X-RAY DIFFRACTION	99
3.0343-3.2686	0.2158	263	0.1825	4877	X-RAY DIFFRACTION	99
3.2686-3.5974	0.1835	259	0.1615	4869	X-RAY DIFFRACTION	99
3.5974-4.1176	0.1856	262	0.146	4911	X-RAY DIFFRACTION	99
4.1176-5.1865	0.148	273	0.1355	4887	X-RAY DIFFRACTION	99
5.1865-44.872	0.1875	272	0.1678	4915	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	8.8061	-6.7682	6.8209	7.9284	-6.3783	6.9321	-0.0869	-0.3902	0.1228	0.8964	-0.1058	-0.269	-0.1357	0.0889	0.2851	0.4188	-0.1056	-0.0198	0.1965	-0.0017	0.157	-2.5913	-41.2315	14.5437
2	1.9264	-0.021	0.0384	1.3736	0.2611	1.9976	0.1311	-0.2451	-0.184	0.3358	-0.0581	0.0063	0.228	0.1483	-0.0787	0.3653	-0.0862	-0.047	0.1738	0.0354	0.1909	2.145	-43.8546	12.1104
3	0.8137	-0.8139	-0.9646	-0.1624	0.345	2.9696	0.0444	-0.3424	0.1364	0.0913	0.0833	0.0766	-0.1165	0.2552	-0.1422	0.3031	-0.1241	0.0445	0.248	-0.0563	0.2109	1.2042	-29.3879	18.9707
4	3.3119	-0.1942	0.0313	3.7533	0.0538	3.5106	-0.4125	-0.6192	-0.5703	0.4039	0.3908	-0.2519	1.0839	0.8926	-0.0247	0.5758	0.2532	0.1127	0.5587	0.0549	0.3494	-3.9813	-43.3721	46.7277
5	1.9584	0.3506	-0.9663	6.6341	3.6497	4.5154	-0.1995	-0.0552	0.0449	-0.2633	0.3258	-0.0757	-0.16	0.3219	-0.1029	0.2473	-0.038	0.0561	0.2982	0.0084	0.192	-9.7574	-28.4906	34.9671
6	2.0508	1.1485	0.4766	1.8865	1.0518	1.6898	0.3339	-0.3363	0.2159	0.3769	-0.1516	0.0922	-0.145	0.0843	-0.1077	0.3564	-0.1337	0.0571	0.2086	-0.0531	0.205	1.5498	-27.3088	11.6093
7	4.8435	-5.8176	5.2969	9.2098	-5.1819	7.5584	0.5418	0.4183	-0.5019	-0.2705	-0.3814	-0.3299	0.3842	0.7607	-0.1232	0.1839	-0.049	0.0339	0.2954	-0.0781	0.3361	22.6357	-30.3227	-7.4843
8	1.4244	0.324	0.0279	3.0236	-1.1482	1.5418	0.1384	-0.1383	-0.0808	0.1506	-0.071	-0.3242	-0.0733	0.3297	-0.0482	0.16	-0.0486	-0.0143	0.2986	-0.0703	0.2323	22.5205	-31.103	-2.1457
9	2.2643	0.4015	-1.6676	0.505	-1.2764	1.085	-0.1846	0.3891	-0.2321	-0.1403	0.0221	-0.0852	0.3839	-0.0054	0.1151	0.2256	-0.0411	0.0017	0.3148	-0.0703	0.1683	16.6015	-38.4702	-14.3062
10	6.1746	-0.25	0.3715	3.7305	-1.4346	5.2727	-0.3823	-0.9492	-0.1458	0.2538	0.1001	-0.256	0.4193	0.3554	0.2445	0.3284	0.1513	0.0256	0.424	0.0033	0.257	44.4848	-45.7519	-21.3057
11	3.81	-1.1789	-4.2869	0.5502	0.7352	3.4949	0.1322	0.4319	0.024	-0.0625	-0.1205	-0.0279	0.1164	-0.3205	0.0195	0.1847	-0.0063	-0.0207	0.3213	-0.0578	0.1607	22.3668	-36.5061	-24.4889
12	3.2822	-0.1937	0.0809	7.8018	5.5139	5.9727	0.1427	0.1549	-0.1752	-0.2607	-0.0774	-0.0975	-0.1224	0.1604	-0.0116	0.1405	-0.0282	0.0202	0.1125	-0.0076	0.1287	7.3588	-39.3662	-8.5719
13	7.1747	-2.7769	3.7339	7.0994	-3.6433	7.9692	-0.1388	0.7016	0.3611	-0.2157	0.0585	-0.1873	-0.3728	0.0082	0.0281	0.2207	-0.0351	0.0546	0.17	0.0366	0.1425	46.9744	-12.5693	-6.5452
14	2.0614	-1.3882	-0.1906	2.5129	-0.1584	0.7736	-0.0454	0.2748	0.0149	-0.2131	0.021	0.0198	0.0561	-0.2036	0.0186	0.1976	-0.0485	-0.0154	0.1751	0.0198	0.1256	37.2616	-7.2385	-6.1851
15	1.8746	0.5458	-1.2427	0.6659	-0.4049	2.1018	0.0733	0.0273	0.0429	-0.0222	-0.0149	-0.102	-0.1009	0.1899	-0.0689	0.1352	0.0098	-0.0037	0.1272	0.0122	0.1624	53.5104	-1.8346	-4.5027
16	3.4056	0.0431	0.0299	4.6102	-1.6426	5.3355	0.0089	-0.017	0.1955	0.0095	0.0584	0.1516	-0.1677	-0.5331	-0.0442	0.1972	0.0536	0.0203	0.2439	0.059	0.1726	53.9934	4.3126	-33.8493
17	5.0821	2.5628	-0.1424	4.228	-0.0261	4.2541	0.0281	-0.1056	-0.0735	-0.053	-0.0398	-0.3085	0.201	0.4679	0.0082	0.1729	0.0645	0.0389	0.2165	0.0202	0.1389	64.7643	-3.8034	-19.7837
18	2.8129	2.3184	-1.033	3.9407	-0.4508	1.7403	0.009	-0.0971	-0.0017	-0.0913	-0.0174	-0.0916	-0.0445	0.1771	0.013	0.1185	0.0156	-0.0085	0.11	0.0117	0.116	51.676	-4.6775	3.1159
19	2.3247	-0.6004	-0.5506	5.2653	-0.0957	3.1777	0.0472	0.041	-0.0055	-0.08	0.1355	0.3337	-0.1117	-0.1548	-0.1067	0.076	0.0133	-0.0008	0.1725	0.0184	0.1371	34.8499	2.3924	26.8525
20	1.417	-0.4505	1.0619	0.2493	-0.4306	3.3995	0.0026	-0.0251	0.1237	-0.1077	0.1045	0.0753	-0.1919	-0.1976	-0.0789	0.1575	0.0067	-0.0127	0.1385	0.0427	0.2164	33.3157	6.8626	14.3892
21	1.3418	0.5417	-0.7971	0.672	0.1207	1.258	-0.0891	0.1004	-0.0621	0.0174	0.0499	0.0319	0.0556	-0.182	0.0307	0.1025	0.0143	-0.0144	0.124	0.0243	0.1411	26.5493	-8.1408	22.3151
22	6.4684	-0.0911	0.0942	1.2907	-0.1813	1.7656	-0.0707	0.1494	0.4744	-0.0617	-0.0556	0.0519	-0.2388	-0.1731	0.1135	0.1538	0.065	-0.0328	0.1982	-0.039	0.1978	5.0468	8.8727	34.3165
23	2.1496	0.5014	-0.6854	3.6654	0.3018	2.4869	-0.0676	-0.0937	-0.1937	0.177	-0.0757	0.0523	0.2073	-0.108	0.1572	0.1203	0.0381	0.0079	0.2001	-0.0168	0.1367	16.4412	-6.7491	38.3092
24	3.8674	1.8719	-0.2058	2.4573	1.0354	1.8656	-0.1213	-0.033	-0.1375	0.0109	0.0812	-0.0469	0.1816	-0.1166	0.0418	0.1147	0.0165	-0.0127	0.1043	0.0413	0.1266	33.8133	-10.5868	18.6892

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:16)
2	X-RAY DIFFRACTION	2	(chain A and resid 17:108)
3	X-RAY DIFFRACTION	3	(chain A and resid 109:182)
4	X-RAY DIFFRACTION	4	(chain A and resid 183:270)
5	X-RAY DIFFRACTION	5	(chain A and resid 271:324)
6	X-RAY DIFFRACTION	6	(chain A and resid 325:363)
7	X-RAY DIFFRACTION	7	(chain B and resid 2:16)
8	X-RAY DIFFRACTION	8	(chain B and resid 17:108)
9	X-RAY DIFFRACTION	9	(chain B and resid 109:188)
10	X-RAY DIFFRACTION	10	(chain B and resid 189:269)
11	X-RAY DIFFRACTION	11	(chain B and resid 270:343)
12	X-RAY DIFFRACTION	12	(chain B and resid 344:364)
13	X-RAY DIFFRACTION	13	(chain C and resid 2:25)
14	X-RAY DIFFRACTION	14	(chain C and resid 26:109)
15	X-RAY DIFFRACTION	15	(chain C and resid 110:183)
16	X-RAY DIFFRACTION	16	(chain C and resid 184:270)
17	X-RAY DIFFRACTION	17	(chain C and resid 271:324)
18	X-RAY DIFFRACTION	18	(chain C and resid 325:364)
19	X-RAY DIFFRACTION	19	(chain D and resid 2:37)
20	X-RAY DIFFRACTION	20	(chain D and resid 38:109)
21	X-RAY DIFFRACTION	21	(chain D and resid 110:183)
22	X-RAY DIFFRACTION	22	(chain D and resid 184:270)
23	X-RAY DIFFRACTION	23	(chain D and resid 271:324)
24	X-RAY DIFFRACTION	24	(chain D and resid 325:364)

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Structure viewers

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Viewer log

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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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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