PDB-4pzl: The crystal structure of adenylate kinase from Francisella tulare...

ID or keywords:

Entry

Database: PDB / ID: 4pzl

Title

The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4

Components

Adenylate kinase

Keywords

TRANSFERASE / structural genomics / The Center for Structural Genomics of Infectious Dis eases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

adenylate kinase / adenylate kinase activity / AMP salvage / ATP binding / cytoplasm
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Mar 31, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4pzl.cif.gz	360.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4pzl_validation.pdf.gz	488.6 KB	Display	wwPDB validaton report
Full document	4pzl_full_validation.pdf.gz	495 KB	Display
Data in XML	4pzl_validation.xml.gz	35.3 KB	Display
Data in CIF	4pzl_validation.cif.gz	49.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzl ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzl	HTTPS FTP

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Related structure data

Similar structure data	4k4x-3 4k4z-4 4k4y-1 4k4x-1 4k4y-3 4k4y-4 4k4y-2 4k4z-3 4k4t-1 3olb-3 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
Other databases	TargetTrack: CSGID-IDP02287

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adenylate kinase

B: Adenylate kinase

C: Adenylate kinase

D: Adenylate kinase

hetero molecules

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

1

A: Adenylate kinase

B: Adenylate kinase

hetero molecules

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

2

C: Adenylate kinase

D: Adenylate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.022, 65.022, 214.732
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

Details

It is predicted that the chain A and B, the chain C and D form dimers respectively.

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase Mass: 27282.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4 / Gene: adk, FTT_1161 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BK21(DE)magic / References: UniProt: Q5NFR4, adenylate kinase

#1: Protein

Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase

Mass: 27282.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: adk, FTT_1161 / Plasmid: pMCSG53 / Production host:

Escherichia coli (E. coli) / Strain (production host): BK21(DE)magic / References: UniProt: Q5NFR4, adenylate kinase

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Non-polymers , 5 types, 297 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.4 Å³/Da / Density % sol: 48.78 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M CaCl2, 0.1M Tris, 20% (w/v) PEG4000., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97924, 0.97938

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: mirror

Radiation

Monochromator: SI 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97924	1
2	0.97938	1

Reflection

Resolution: 2.1→34.5 Å / Num. all: 59141 / Num. obs: 59141 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.8 % / B_iso Wilson estimate: 48.9 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 30.1

Reflection shell

Resolution: 2.1→2.14 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.664 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2896 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.1→34.148 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 26.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2368	2985	5.05 %	random
R_work	0.1913	-	-	-
all	0.1936	59075	-	-
obs	0.1936	59075	99.62 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→34.148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6800	0	33	288	7121

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6929
X-RAY DIFFRACTION	f_angle_d	1.089	9374
X-RAY DIFFRACTION	f_dihedral_angle_d	13.359	2574
X-RAY DIFFRACTION	f_chiral_restr	0.075	1104
X-RAY DIFFRACTION	f_plane_restr	0.005	1223

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 (%)
2.0992-2.1336	0.3726	149	0.2801	2642	X-RAY DIFFRACTION	100
2.1336-2.1704	0.2962	134	0.2617	2718	X-RAY DIFFRACTION	100
2.1704-2.2098	0.3171	143	0.2452	2636	X-RAY DIFFRACTION	100
2.2098-2.2523	0.3097	154	0.238	2715	X-RAY DIFFRACTION	100
2.2523-2.2983	0.2623	131	0.219	2661	X-RAY DIFFRACTION	100
2.2983-2.3482	0.2901	141	0.2249	2668	X-RAY DIFFRACTION	100
2.3482-2.4028	0.2512	137	0.2246	2716	X-RAY DIFFRACTION	100
2.4028-2.4629	0.2514	127	0.2176	2686	X-RAY DIFFRACTION	100
2.4629-2.5295	0.294	145	0.226	2667	X-RAY DIFFRACTION	100
2.5295-2.6039	0.2869	144	0.2298	2714	X-RAY DIFFRACTION	100
2.6039-2.6879	0.2928	152	0.2351	2658	X-RAY DIFFRACTION	100
2.6879-2.7839	0.2866	138	0.2337	2656	X-RAY DIFFRACTION	100
2.7839-2.8953	0.2728	129	0.2229	2727	X-RAY DIFFRACTION	100
2.8953-3.027	0.2606	161	0.2203	2660	X-RAY DIFFRACTION	100
3.027-3.1865	0.2554	151	0.2168	2670	X-RAY DIFFRACTION	100
3.1865-3.386	0.2643	144	0.2083	2695	X-RAY DIFFRACTION	100
3.386-3.6472	0.2478	145	0.1907	2665	X-RAY DIFFRACTION	100
3.6472-4.0137	0.2203	130	0.1688	2689	X-RAY DIFFRACTION	100
4.0137-4.5933	0.1968	146	0.1499	2688	X-RAY DIFFRACTION	100
4.5933-5.7825	0.2036	156	0.1601	2652	X-RAY DIFFRACTION	100
5.7825-34.1529	0.194	128	0.1742	2507	X-RAY DIFFRACTION	93

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	3.1153	-1.6261	0.4041	7.0565	-2.3839	2.7573	0.1063	-0.0418	-0.0845	0.6279	0.366	0.3757	-0.0651	-0.3063	-0.4688	0.32	0.0353	0.0405	0.4046	0.0099	0.3129	61.3082	27.1037	14.9731
2	2.8446	0.6305	1.8023	3.7138	2.6863	6.5475	0.4193	1.2546	-0.2219	-0.2539	0.3408	-0.767	-0.1667	0.1965	-0.7397	0.4439	0.0319	-0.0943	0.833	0.0144	0.4371	58.9613	25.5606	-7.6561
3	3.5278	-1.2008	-1.6063	3.7691	-0.3531	2.2018	0.4244	0.55	-0.0844	-0.2626	-0.2961	0.5341	-0.0164	-0.8678	-0.1263	0.3087	0.0344	-0.0284	0.6864	0.0579	0.5245	51.3402	26.9856	4.0841
4	3.7574	-0.3628	-3.3813	1.5022	-1.1436	4.2145	-0.0389	-0.5822	-0.2928	0.3119	0.3565	0.8668	-0.3227	-0.0612	-0.3179	0.6656	0.1715	0.2454	0.5123	0.132	0.5128	69.4658	53.209	-2.6405
5	2.5788	2.3672	-1.3264	3.3094	-2.7998	2.865	0.4632	0.4186	0.2899	0.4498	0.3861	0.7826	-0.5841	-0.7628	-0.5664	0.4726	0.2497	0.1606	0.7456	0.2865	1.0935	46.5281	42.878	4.1152
6	4.4821	1.1057	1.5545	7.5202	0.8526	3.4149	0.1317	-0.3834	0.6908	0.4964	0.148	1.6923	-0.1817	-0.9094	-0.4533	0.5193	0.1092	0.1896	0.6975	0.0718	0.7414	47.342	34.0737	15.3568
7	6.2207	1.5624	-0.2309	2.078	-0.1069	6.9628	0.5368	-0.8833	0.4897	1.2307	0.2363	-0.3445	-0.715	0.156	-0.5595	0.5725	0.18	0.0455	0.4191	-0.1173	0.4918	59.8859	37.4257	22.0465
8	3.6386	0.5996	-1.5614	1.5796	-1.129	4.932	0.1133	-0.1784	-0.2344	0.081	-0.2313	0.1206	0.4649	-0.5124	0.1202	0.3799	-0.0653	-0.0141	0.2105	-0.0732	0.2951	72.4163	17.3173	6.3305
9	3.4916	1.1802	1.7018	3.0169	0.0888	2.9301	-0.0366	-0.1992	0.7674	0.3683	-0.1801	0.0962	-0.597	0.2118	0.2423	0.4516	-0.0552	-0.0469	0.249	-0.0589	0.3974	80.0639	37.4309	11.4439
10	9.1035	-2.0727	-4.1361	2.6859	-0.5136	6.7779	0.1486	-0.2208	0.3634	-0.0839	0.1807	-0.1689	-0.2459	0.4364	-0.3946	0.3376	-0.0436	-0.013	0.2154	-0.0593	0.3078	77.8689	24.9865	9.4856
11	4.1342	-2.0647	-1.4224	4.433	-2.6152	4.6059	0.141	-0.5669	0.1721	0.318	-0.1677	-0.5687	0.2465	0.3529	0.0822	0.2716	0.0043	-0.0264	0.169	-0.0197	0.3732	86.9337	21.7736	6.0977
12	6.9525	-4.7576	-2.4595	3.3338	1.4969	1.8795	0.6902	0.3872	-0.3982	-1.4471	-0.5951	0.5544	-0.0347	-0.3278	-0.0137	0.5935	0.1567	0.0102	0.5643	-0.039	0.5039	73.5748	35.2836	-16.6793
13	1.697	-1.3713	-1.1141	6.2503	1.4779	5.7389	1.1121	0.5059	-0.2797	-1.526	-0.9145	0.6292	-0.2617	-0.6154	-0.1831	0.8405	0.2314	-0.1583	0.6426	-0.0539	0.553	69.7968	40.1841	-20.3943
14	5.1529	-3.4129	3.813	6.0945	-5.214	4.6627	0.0296	0.5139	0.5466	-0.5113	-0.5556	-1.0761	0.1384	1.0957	0.5722	0.3664	0.0294	0.0924	0.4049	-0.0051	0.4816	90.2385	27.6113	-6.2337
15	5.8418	-1.3966	0.6743	6.1844	-2.4374	5.8374	0.0233	-0.1557	-0.2227	-0.2867	-0.1791	-0.1914	0.978	0.1066	0.0813	0.4024	0.0915	0.024	0.2218	-0.0705	0.3172	81.0289	12.8754	-0.3312
16	4.6746	-0.4335	0.5414	5.4985	-1.2349	1.5806	0.0282	0.2599	-0.4118	0.0191	0.1984	0.3058	0.2688	-0.5884	-0.2304	0.2731	-0.0483	-0.079	0.5	0.0196	0.2283	64.4376	1.3363	48.4396
17	1.0081	-0.4403	-1.5912	3.0499	-3.7505	9.3377	-0.054	0.3988	0.2563	-0.2125	0.2032	0.1096	-0.3817	-0.1686	-0.1828	0.3767	-0.084	-0.0891	0.5191	0.0545	0.3852	66.1161	14.7854	32.1081
18	1.6302	-1.0012	-0.7543	3.1869	-1.8146	2.3779	-0.1329	0.2574	0.2646	-0.4764	0.2018	-0.0455	-0.4682	0.1949	-0.096	0.3759	-0.1325	-0.0564	0.5219	-0.0375	0.3602	72.2885	16.5298	37.0561
19	1.3449	0.1132	0.6853	3.8286	1.1482	3.9555	0.1085	-0.2396	-0.0725	0.032	-0.0383	-0.1639	-0.1502	0.0826	-0.0888	0.2064	-0.01	-0.0596	0.3496	-0.0127	0.2215	72.1254	9.1627	47.5389
20	8.9574	-2.353	6.6393	1.5956	-1.8463	4.8578	-0.3469	-0.8687	0.4558	0.2338	0.3019	-0.5473	0.2465	-0.8559	0.0449	0.5923	-0.1018	-0.1162	0.5744	-0.1544	0.4526	68.2082	-12.882	30.2108
21	4.8011	-0.9159	3.0593	2.7652	0.6965	5.1514	0.6574	-0.904	-0.118	0.7236	-0.2103	-0.2711	0.3441	0.2645	-0.3323	0.6616	-0.2449	-0.1646	0.6893	-0.0819	0.4727	63.9757	-16.377	25.1335
22	0.8942	0.1554	-0.6578	5.3274	4.5295	5.7414	0.0617	0.4852	-0.8823	-0.2005	0.4976	-0.1884	0.3888	0.4418	-0.4456	0.3777	0.0019	-0.1065	0.6658	-0.2063	0.6199	81.9347	-1.8726	41.7668
23	2.4087	2.6352	1.2853	6.1371	3.141	4.1701	0.1355	-0.2429	-0.3946	0.6992	0.2822	-0.1137	0.6278	0.0409	-0.3954	0.3876	-0.0114	-0.137	0.4609	0.0559	0.3418	71.5092	-0.4996	55.3028
24	4.8905	0.771	2.2556	4.6809	0.2743	4.1273	-0.1528	-0.363	-0.2778	-0.1382	0.4459	0.4922	-0.2373	-0.9825	-0.0596	0.2911	-0.0203	-0.1153	0.6698	0.1456	0.406	49.2001	11.7436	37.0566
25	6.6698	0.7816	1.7665	3.1759	-0.7651	2.9212	0.2959	-0.4553	-1.5063	-0.2549	0.2672	0.2748	0.8909	-0.6224	-0.5179	0.5168	-0.1983	-0.1887	0.7543	0.2141	0.8335	47.5733	-4.7405	41.3688
26	1.032	0.1776	-0.472	1.8679	0.3487	1.1259	-0.008	-0.859	-0.2938	-0.1619	-0.1576	1.0833	0.1295	-1.0433	-0.4813	0.2167	-0.1873	-0.3272	1.386	0.459	0.964	37.4764	5.928	37.4335
27	2.5167	0.5546	0.3934	2.6956	0.1896	2.057	-0.2339	0.3577	0.134	-0.9658	0.4157	0.0728	-0.2079	0.1035	-0.2001	0.7075	-0.2691	-0.0748	0.5335	-0.042	0.4815	61.9179	2.8492	13.9244
28	1.0052	-0.3794	-0.1572	1.1554	-0.6902	0.6267	0.095	-0.6768	-0.4963	-0.2772	0.2524	0.6076	0.518	-1.1322	0.1771	0.4631	-0.2997	-0.4595	1.0152	0.2311	0.8757	38.4863	3.4209	23.7884
29	0.4538	1.2132	0.2684	3.0905	0.5579	2.0902	-0.3755	0.2793	0.4328	0.0954	0.5448	1.1717	-0.4739	-1.4735	0.0105	0.511	0.0658	-0.138	1.202	0.2628	0.8269	36.5404	13.6154	35.0003
30	2.3356	-2.1047	-3.3903	8.412	1.7491	8.6191	-0.023	-0.5539	1.0955	-0.3194	0.8015	0.8303	-1.2826	-0.9957	-0.5769	0.5443	0.1115	-0.2283	0.739	0.0799	0.7715	47.4888	22.1587	34.7764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -9 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 112 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 113 through 160 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 161 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 203 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 204 through 217 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -9 through 26 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 27 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 112 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 113 through 134 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 135 through 160 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 161 through 183 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 184 through 218 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid -1 through 26 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 27 through 54 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 55 through 73 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 74 through 112 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 113 through 131 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 132 through 160 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 161 through 183 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 184 through 217 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 0 through 26 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 27 through 89 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 90 through 112 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 113 through 160 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 161 through 183 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 184 through 203 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 204 through 217 )

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