PDB-4ktb: The crystal structure of posible asymmetric diadenosine tetraphos...

ID or keywords:

Entry

Database: PDB / ID: 4ktb

Title

The crystal structure of posible asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases from Jonesia denitrificans DSM 20603

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Protein of unknown function DUF4916 / Domain of unknown function (DUF4916) / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / hydrolase activity / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein

Function and homology information

Biological species

Jonesia denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.936 Å

Authors

Tan, K. / Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of posible asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases from Jonesia denitrificans DSM 20603
Authors: Tan, K. / Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A.

History

Deposition	May 20, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 5, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ktb.cif.gz	268.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ktb.ent.gz	230.1 KB	Display	PDB format
PDBx/mmJSON format	4ktb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ktb_validation.pdf.gz	474.9 KB	Display	wwPDB validaton report
Full document	4ktb_full_validation.pdf.gz	484.4 KB	Display
Data in XML	4ktb_validation.xml.gz	31.1 KB	Display
Data in CIF	4ktb_validation.cif.gz	45.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/4ktb ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4ktb	HTTPS FTP

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Related structure data

Similar structure data	2frv-4 1ubo-d 2frv-2 2zki-2 4dy4-1 4ueq-3 1frv-2 1wuh-d 1ubm-d 2frv-1 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: MCSG-APC103520

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (1) #201 - Sep 2016 Isoprene Synthase similarity (1)

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

D: Putative uncharacterized protein

hetero molecules

87.9 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)	55.489, 69.809, 94.313
Angle α, β, γ (deg.)	90.00, 90.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Experimentally unknown. It is predicted that the chains A,B,C and D form a tetramer.

#1: Protein	Putative uncharacterized protein Mass: 21761.641 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Jonesia denitrificans (bacteria) / Strain: DSM 20603 / Gene: Jden_0890 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7R2I1
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.1 Å³/Da / Density % sol: 41.39 %
Crystal grow	Temperature: 289 K / pH: 8.5 Details: 3.0M Sodium Chloride, 0.1M Tris:HCl, pH 8.5, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97897 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97897 Å / Relative weight: 1
Reflection twin	Operator: h,-k,-l / Fraction: 0.48
Reflection	Resolution: 1.95→50 Å / Num. all: 52824 / Num. obs: 52824 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / R_merge(I) obs: 0.101 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.623 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2603 / % possible all: 97.9

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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: 1.8.1_1168)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.936→47.839 Å / σ(F): 0 / Phase error: 24.59 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2238	2037	4.18 %	random
R_work	0.1726	-	-	-
all	0.1784	48781	-	-
obs	0.1784	48781	90.64 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.936→47.839 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4920	0	27	510	5457

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5111
X-RAY DIFFRACTION	f_angle_d	1.178	6986
X-RAY DIFFRACTION	f_dihedral_angle_d	15.208	1927
X-RAY DIFFRACTION	f_chiral_restr	0.067	795
X-RAY DIFFRACTION	f_plane_restr	0.007	924

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 (%)
1.939-1.9875	0.3084	62	0.2603	1478	X-RAY DIFFRACTION	39
1.9875-2.0413	0.273	108	0.2444	2481	X-RAY DIFFRACTION	66
2.0413-2.1013	0.2621	135	0.2362	3032	X-RAY DIFFRACTION	79
2.1013-2.1691	0.3096	142	0.2216	3359	X-RAY DIFFRACTION	89
2.1691-2.2467	0.2484	151	0.2076	3596	X-RAY DIFFRACTION	94
2.2467-2.3366	0.227	153	0.2004	3624	X-RAY DIFFRACTION	95
2.3366-2.443	0.307	153	0.1896	3638	X-RAY DIFFRACTION	96
2.443-2.5718	0.2182	153	0.1978	3620	X-RAY DIFFRACTION	96
2.5718-2.7329	0.2575	152	0.1859	3690	X-RAY DIFFRACTION	96
2.7329-2.9438	0.2377	157	0.1772	3670	X-RAY DIFFRACTION	96
2.9438-3.24	0.1917	156	0.1631	3660	X-RAY DIFFRACTION	96
3.24-3.7087	0.1881	159	0.1411	3662	X-RAY DIFFRACTION	95
3.7087-4.672	0.1774	156	0.1262	3605	X-RAY DIFFRACTION	94
4.672-47.8535	0.2888	154	0.1669	3659	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	1.1783	-0.3824	-0.3377	1.867	0.2243	0.7052	-0.0535	0.0542	0.1321	0.0619	-0.0703	0.1753	-0.3218	-0.3386	0.1336	0.0833	0.0026	0.0319	0.0401	0.0085	0.1305	30.2209	24.9263	80.5847
2	1.7939	0.2558	-0.2075	2.2879	1.2963	0.8576	0.2894	-0.4914	0.6661	0.3485	-0.1129	0.0769	-0.3113	-0.1767	-0.1401	0.2513	0.0176	0.1004	0.1701	-0.0702	0.3548	29.5286	33.2658	89.5698
3	1.8005	-0.051	-0.0038	0.6429	-0.2885	1.0661	0.0674	0.0086	0.0826	0.0868	-0.0544	0.0998	-0.0745	-0.1489	0.0237	0.0708	-0.0135	-0.0057	0.0677	-0.0155	0.0609	33.9699	20.0884	85.1666
4	3.069	0.2136	-0.4254	3.363	1.6868	3.0697	-0.05	0.0083	0.1394	0.2557	-0.2798	0.3649	0.0583	-0.5112	0.1476	0.1056	-0.0033	0.0242	0.1315	-0.0215	0.2712	18.8148	25.9144	83.48
5	1.2332	0.2801	-0.1254	1.1136	0.1786	1.2587	0.0583	0.1769	0.5419	-0.1436	-0.141	0.1176	-0.3049	-0.1646	-0.0316	0.1793	0.0433	0.0127	0.1097	0.0459	0.2366	32.7252	33.9346	75.0941
6	2.0655	-0.5207	-0.0498	2.2381	0.2471	1.4965	0.1031	-0.02	-0.3609	0.2202	-0.0664	-0.0294	0.1908	0.2408	0.0075	0.0707	0.0119	-0.0352	0.088	-0.0259	0.1416	53.6154	3.1309	83.284
7	1.4695	0.0958	-1.6478	1.5731	1.8822	4.3723	-0.1098	-0.0211	-0.1072	0.3462	-0.025	-0.3275	0.0977	0.0316	-0.1139	0.1004	0.0289	0.0264	-0.0826	-0.0181	0.193	50.7405	21.0356	92.042
8	0.0701	-0.1545	0.022	0.8311	0.2013	0.3768	0.0753	-0.0055	0.0742	-0.0854	0.0056	-0.1769	0.0163	0.0931	0.1834	0.0667	0.0183	-0.0139	-0.0811	0.0741	0.1372	56.1864	14.6843	81.5889
9	2.4446	1.7112	-2.189	2.3453	-1.0763	3.0063	-0.0801	-0.1279	-0.1524	0.1638	0.0059	0.0899	0.2717	0.0006	0.0543	0.1059	0.0362	-0.0161	0.0291	0.0122	0.1425	42.3127	5.44	86.7511
10	2.5301	2.3968	-2.6815	5.6803	-6.4193	9.2342	0.3136	-0.3263	-0.0736	0.3299	-0.3619	-0.233	-0.4665	0.5737	0.1267	0.1657	0.0003	-0.0362	0.2414	-0.0258	0.1989	64.4492	5.2649	83.5409
11	1.4225	-0.6966	-0.4836	0.905	-0.0827	1.1107	0.1148	0.2429	-0.5444	-0.0787	-0.0348	0.2783	0.4967	0.0561	0.1341	0.1858	0.047	-0.0371	0.1151	-0.0823	0.2182	50.4839	-2.5077	75.4352
12	0.6882	0.1345	0.3601	0.9391	0.3439	2.0287	-0.0303	0.3437	0.2335	-0.2533	-0.2452	-0.0251	-0.1791	0.3028	-0.2135	0.1887	-0.0263	0.0381	0.2835	0.19	0.0939	52.045	25.941	60.9601
13	1.0782	-0.4498	-0.5232	0.6961	-0.2071	0.6107	-0.0159	0.636	0.5472	-0.7688	-0.028	0.1929	-0.4541	0.0418	-0.0596	0.6044	-0.0007	0.0089	0.4182	0.2531	0.2567	52.3669	34.5731	51.8712
14	0.3608	0.4262	0.4635	0.71	0.2957	0.9368	0.0151	0.6392	0.0116	-0.302	-0.0013	-0.2213	-0.1606	0.1873	0.067	0.2091	0.0818	0.0234	0.3495	0.0739	0.0312	48.8309	20.5482	56.0915
15	2.0768	-0.9334	-0.4731	3.2295	-1.5701	2.8178	0.0013	0.4537	0.332	-0.3837	-0.1083	-0.2225	-0.2196	0.4882	0.0411	0.2784	-0.0709	0.0073	0.4889	0.188	0.3071	59.5709	32.1322	62.6456
16	0.6805	0.8825	-0.3056	1.6638	-1.2463	2.0602	-0.0195	0.2395	0.4398	-0.1094	-0.2188	-0.1074	-0.4792	0.1083	0.0208	0.2432	0.0638	0.013	0.1866	0.1263	0.2185	46.0468	34.1493	65.882
17	0.3163	-0.0314	-0.2579	0.6249	-0.3487	2.0248	-0.0262	0.5783	-0.2155	-0.1563	-0.0363	0.0879	0.0798	-0.2745	0.0616	0.1368	0.0382	-0.0635	0.4133	-0.1069	0.1541	30.6767	5.3516	61.766
18	3.3194	1.0523	1.8307	5.2359	0.5479	2.0201	0.2637	0.5656	-0.7571	-0.4019	0.0575	-0.1276	0.4581	-0.2986	-0.4939	0.281	-0.0493	-0.0892	0.7477	-0.2203	0.311	30.9088	-3.1379	51.7992
19	0.6554	0.1145	-0.2885	1.1837	-0.8754	0.9401	0.017	0.361	-0.0219	-0.3245	0.0404	0.1377	0.1919	-0.1844	0.0716	0.2409	0.0305	-0.1162	0.4904	-0.0768	0.0986	28.1027	15.4547	53.539
20	0.5927	0.2701	0.2796	0.793	-0.3574	0.5575	0.0204	0.3948	-0.16	-0.3126	-0.0642	0.0913	0.1434	-0.1943	0.0762	0.2287	0.064	-0.0523	0.4006	-0.1105	0.0804	37.6166	8.1356	57.6616
21	0.5519	0.4378	0.2289	0.8205	0.3638	1.1238	0.0201	0.548	-0.389	-0.0938	-0.0316	0.1016	0.3625	-0.3755	-0.1141	0.2413	-0.0343	-0.0413	0.3849	-0.1458	0.2367	30.031	-1.2856	63.1735
22	3.2481	-1.3847	-0.604	4.4712	-0.4237	4.6256	0.089	-0.1128	-0.6206	0.5216	-0.0903	0.1249	0.6616	-0.0706	0.0922	0.2366	-0.047	-0.113	0.1611	-0.0072	0.2501	36.8634	-2.2322	75.7362

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 191 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 33 through 76 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 77 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 110 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 111 through 139 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 151 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 152 through 190 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 32 through 62 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 63 through 76 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 77 through 139 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 140 through 163 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 164 through 191 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 33 through 62 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 63 through 76 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 77 through 95 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 96 through 139 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 140 through 184 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 185 through 191 )

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