PDB-4yov: Crystal structure of a trimeric exonuclease PhoExo I from Pyrococ...

ID or keywords:

Entry

Database: PDB / ID: 4yov

Title

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA

Components

3-5 exonuclease PhoExo I
5'-D(*AP*AP*AP*AP*AP*AP*A)-3'

Keywords

HYDROLASE/DNA / exonuclease / HYDROLASE-DNA complex

Function / homology

Function and homology information

exonuclease activity / metal ion binding
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.05 Å

Authors

Miyazono, K. / Ito, T. / Tanokura, M.

Funding support

Japan, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I
Authors: Miyazono, K. / Ishino, S. / Tsutsumi, K. / Ito, T. / Ishino, Y. / Tanokura, M.

History

Deposition	Mar 12, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	Feb 5, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy Category: citation / diffrn_source ...citation / diffrn_source / pdbx_entity_src_syn / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4yov.cif.gz	296.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4yov.ent.gz	242.5 KB	Display	PDB format
PDBx/mmJSON format	4yov.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4yov_validation.pdf.gz	461.3 KB	Display	wwPDB validaton report
Full document	4yov_full_validation.pdf.gz	470.6 KB	Display
Data in XML	4yov_validation.xml.gz	26.1 KB	Display
Data in CIF	4yov_validation.cif.gz	35.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/4yov ftp://data.pdbj.org/pub/pdb/validation_reports/yo/4yov	HTTPS FTP

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Related structure data

Related structure data	4yorC 4yotC 4youC 4yowC 4yoxC 4yoyC C: citing same article (ref.)
Similar structure data	4yox-d 4yoy-d 4yow-d 5chi-d 4you-d 4yor-1 4jf9-1 2arh-d 4goq-d 3azb-2 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

Deposited unit

A: 3-5 exonuclease PhoExo I

B: 5'-D(*AP*AP*AP*AP*AP*AP*A)-3'

C: 3-5 exonuclease PhoExo I

D: 5'-D(*AP*AP*AP*AP*AP*AP*A)-3'

E: 3-5 exonuclease PhoExo I

F: 5'-D(*AP*AP*AP*AP*AP*AP*A)-3'

85.1 kDa, 6 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)	94.676, 95.099, 105.266
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	3-5 exonuclease PhoExo I Mass: 26219.281 Da / Num. of mol.: 3 / Mutation: D80N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A060P168
#2: DNA chain	5'-D(APAPAPAPAPAPA)-3' Mass: 2147.490 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.84 Å³/Da / Density % sol: 56.68 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: MES, PEG6000, LiCl

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-5A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.05→70.567 Å / Num. all: 59879 / Num. obs: 59879 / % possible obs: 99.3 % / Redundancy: 6.7 % / B_iso Wilson estimate: 36.39 Å² / R_pim(I) all: 0.024 / R_rim(I) all: 0.062 / R_sym value: 0.058 / Net I/av σ(I): 8.875 / Net I/σ(I): 17.1 / Num. measured all: 403350

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.05-2.16	4.3	0.485	1.6	36288	8347	0.259	0.485	2.8	96.4
2.16-2.29	6.6	0.368	2.1	54517	8211	0.154	0.368	4.8	100
2.29-2.45	7.4	0.271	2.8	57600	7767	0.106	0.271	6.7	100
2.45-2.65	7.4	0.186	4.1	53637	7238	0.073	0.186	9.3	100
2.65-2.9	7.4	0.119	6.3	49259	6680	0.047	0.119	13.4	100
2.9-3.24	7.3	0.07	10	44124	6059	0.028	0.07	21.2	100
3.24-3.74	7.1	0.046	13.4	38410	5387	0.019	0.046	32.3	100
3.74-4.58	7	0.037	15.5	32024	4589	0.015	0.037	42.4	100
4.58-6.48	6.7	0.035	16.5	24253	3601	0.014	0.035	44	100
6.48-19.8	6.6	0.029	19.6	13238	2000	0.012	0.029	48	96.2

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Resolution: 2.05→19.8 Å / FOM work R set: 0.7619 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 29.18 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection
R_free	0.2325	5719	5.04 %
R_work	0.191	107861	-
obs	0.1931	59783	98.69 %

Solvent computation

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

Displacement parameters

B_iso max: 175.48 Å² / B_iso mean: 70.57 Å² / B_iso min: 25.68 Å²

Refinement step

Cycle: final / Resolution: 2.05→19.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5328	252	0	129	5709
B_iso mean	-	-	-	52.65	-
Num. residues	-	-	-	-	688

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5709
X-RAY DIFFRACTION	f_angle_d	1.122	7763
X-RAY DIFFRACTION	f_chiral_restr	0.049	886
X-RAY DIFFRACTION	f_plane_restr	0.006	937
X-RAY DIFFRACTION	f_dihedral_angle_d	13.079	2174

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.05-2.0733	0.4316	194	0.3882	3035	3229	84
2.0733-2.0976	0.363	182	0.3533	3336	3518	92
2.0976-2.1232	0.3469	179	0.3295	3373	3552	93
2.1232-2.15	0.3252	174	0.3052	3562	3736	96
2.15-2.1783	0.305	203	0.29	3511	3714	98
2.1783-2.2081	0.2893	186	0.2699	3689	3875	100
2.2081-2.2396	0.2616	211	0.2569	3588	3799	100
2.2396-2.273	0.2813	164	0.2489	3676	3840	100
2.273-2.3084	0.2938	189	0.2419	3682	3871	100
2.3084-2.3462	0.3065	160	0.2415	3591	3751	100
2.3462-2.3866	0.2862	236	0.2368	3633	3869	100
2.3866-2.4299	0.2664	175	0.2243	3674	3849	100
2.4299-2.4766	0.2822	199	0.2137	3593	3792	100
2.4766-2.527	0.2409	177	0.2128	3671	3848	100
2.527-2.5819	0.2684	192	0.212	3670	3862	100
2.5819-2.6418	0.2891	200	0.217	3616	3816	100
2.6418-2.7077	0.2919	137	0.2282	3688	3825	100
2.7077-2.7807	0.2538	176	0.2153	3693	3869	100
2.7807-2.8623	0.2637	193	0.2063	3603	3796	100
2.8623-2.9544	0.2405	233	0.211	3615	3848	100
2.9544-3.0597	0.2448	198	0.1982	3626	3824	100
3.0597-3.1817	0.2357	203	0.2033	3622	3825	100
3.1817-3.3258	0.2371	232	0.1961	3604	3836	100
3.3258-3.5003	0.2265	185	0.1956	3674	3859	100
3.5003-3.7182	0.2375	206	0.1798	3627	3833	100
3.7182-4.0031	0.1816	212	0.1659	3600	3812	100
4.0031-4.402	0.1979	175	0.1502	3670	3845	100
4.402-5.0298	0.197	178	0.1407	3670	3848	100
5.0298-6.3029	0.2027	190	0.1585	3621	3811	100
6.3029-19.8014	0.176	180	0.1441	3648	3828	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	2.8691	0.5845	0.8264	2.4796	-0.0159	1.5386	-0.0361	0.1722	0.4072	-0.1167	-0.1656	0.097	-0.2393	-0.1917	0.1569	0.3435	0.0135	-0.0549	0.4328	0.0459	0.4587	17.9089	29.7984	4.2855
2	3.5845	-0.4614	0.8822	2.669	-1.4558	0.9056	-0.4601	-0.5674	1.0169	0.3805	0.2273	0.162	-0.5814	-0.6064	0.2295	0.4539	0.1508	-0.1459	0.7248	-0.1581	0.7545	2.5072	29.9823	11.1421
3	2.9768	0.4858	0.1669	1.7907	-0.7903	1.5856	-0.0447	0.56	-0.0363	-0.1802	-0.0505	-0.1122	0.0281	0.0416	0.1138	0.2874	-0.0056	-0.0306	0.4099	-0.016	0.3169	27.5195	24.2893	2.0882
4	3.0337	-1.5096	0.1559	2.2742	2.0002	3.5273	-0.0469	0.4476	0.1907	-0.2854	0.0726	-0.3027	-0.5385	0.3242	0.0915	0.3069	-0.0691	-0.0251	0.3732	0.013	0.4818	34.5463	30.7623	8.95
5	1.6389	-1.3599	-0.2875	1.8497	1.1633	1.2292	-0.451	-0.8479	0.4446	0.9326	-0.2955	0.9011	0.0143	-0.2449	0.7352	0.8658	0.1668	0.0304	0.9873	0.0122	1.3068	17.8695	33.1124	16.1459
6	2.1252	-0.2368	0.3114	2.0256	-0.7812	2.1569	-0.0096	-0.3499	-0.0609	0.6881	0.062	-0.2626	-0.1507	0.104	-0.0561	0.5047	-0.0296	-0.1522	0.3187	0.0205	0.3958	43.2927	23.9869	32.6953
7	1.5124	0.0521	0.8317	2.9277	0.6933	2.3274	-0.0811	-0.3964	0.3228	0.7209	-0.1001	0.6075	-0.0719	-0.363	0.0312	0.598	-0.0326	-0.0132	0.4028	-0.0941	0.7602	37.2978	39.8999	33.6595
8	2.1127	-0.3414	0.5533	2.2365	-0.9	2.0634	-0.0374	-0.1055	-0.3185	0.2422	-0.0215	-0.3511	0.1339	0.1353	0.0321	0.3773	-0.0095	-0.1408	0.246	0.0366	0.495	44.8311	14.5082	27.1968
9	1.8128	-0.3678	-1.0449	1.8147	0.7914	1.7146	-0.3574	-0.7551	-0.5772	0.304	0.2441	0.0839	0.2272	-0.1536	0.0234	0.4573	0.0101	-0.0717	0.3516	0.1675	0.6186	38.1652	7.6778	33.8978
10	0.1387	-0.268	-0.2617	0.5287	0.5331	0.5381	0.7015	-0.6772	0.9835	0.5461	-0.1749	0.1712	-0.8469	-0.7733	-0.3601	1.5	0.0697	-0.1678	0.9725	0.0111	1.4891	31.7381	24.6746	36.8801
11	0.025	-0.0951	-0.1263	0.9444	-0.1047	1.785	-0.1528	-0.5132	-0.8783	0.1945	-0.0109	0.4304	0.1644	-0.8132	-0.8094	0.4932	-0.2108	-0.0011	0.6833	0.5065	1.1033	13.495	1.8645	27.2727
12	1.6303	0.3978	0.5301	1.5657	-0.2607	1.1832	0.132	-0.909	-0.6526	0.4387	0.2098	0.7735	0.3572	-0.8897	-0.165	0.6757	-0.1655	0.0982	0.9095	0.347	1.1738	13.4985	-2.2599	33.7463
13	1.082	0.4044	-0.2287	0.4026	0.5709	1.6652	0.0516	-0.8602	0.0478	0.7983	-0.1897	0.815	-0.1197	-0.8335	-0.0851	0.8966	-0.0045	0.3173	1.2097	0.2673	0.9566	14.1232	8.7856	45.5959
14	0.9154	-0.0905	0.7835	0.9418	-0.9212	1.4635	0.2965	-0.1222	-1.117	-0.074	0.0338	0.2289	0.6224	-0.3786	-0.1708	0.5299	-0.1496	-0.1244	0.4582	0.0524	0.9673	17.2968	-0.1173	17.8121
15	0.0748	-0.0788	-0.0576	0.0892	0.0589	0.0415	-0.258	-0.7962	0.05	0.5581	0.8329	0.5052	-0.5611	-1.3734	-0.3072	0.9681	-0.0353	0.1878	1.1233	0.1899	1.0314	10.1668	12.0557	29.2698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 56 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 138 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 139 through 213 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 214 through 229 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 4 )	B
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 55 )	C
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 56 through 138 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 139 through 213 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 214 through 229 )	C
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 4 )	D
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 1 through 31 )	E
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 32 through 72 )	E
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 73 through 138 )	E
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 139 through 227 )	E
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 1 through 4 )	F

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