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

ID or keywords:

Entry

Database: PDB / ID: 4yot

Title

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 2.15A resolution

Components

3-5 exonuclease PhoExo I

Keywords

HYDROLASE /

exonuclease

Function / homology

Protein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) /

exonuclease activity /

Nucleotidyltransferase; domain 5 / 2-Layer Sandwich /

metal ion binding / Alpha Beta / 3-5 exonuclease PhoExo I

Function and homology information

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Miyazono, K. / Tsutsumi, K. / 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 / Derived calculations Category: citation / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yot.cif.gz	282 KB	Display	PDBx/mmCIF format
PDB format	pdb4yot.ent.gz	229.9 KB	Display	PDB format
PDBx/mmJSON format	4yot.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/4yot ftp://data.pdbj.org/pub/pdb/validation_reports/yo/4yot	HTTPS FTP

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Related structure data

Related structure data	4yorC 4youC 4yovC 4yowC 4yoxC 4yoyC C: citing same article (ref.)
Similar structure data	4o8u-1 4o8u-2 4you-d 6j55-2 4yor-1 3jqy-d 3tl3-1 2c2w-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 3-5 exonuclease PhoExo I

B: 3-5 exonuclease PhoExo I

C: 3-5 exonuclease PhoExo I

hetero molecules

77.1 kDa, 3 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)	94.610, 94.820, 99.710
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: 25667.678 Da / Num. of mol.: 3 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: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.9 Å³/Da / Density % sol: 57.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: polyethylene glycol monomethyl ether 550

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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: Oct 26, 2008

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.15→20 Å / Num. obs: 49267 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 36.35 Å² / R_merge F obs: 0.1 / R_merge(I) obs: 0.084 / R_rim(I) all: 0.091 / Χ²: 1.012 / Net I/σ(I): 13.05 / Num. measured all: 337105

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.15-2.21		0.722	0.634	2.6	16200	3609	3559	0.72	98.6
2.21-2.27		0.42	0.453	4.22	22099	3499	3496	0.494	99.9
2.27-2.33		0.325	0.382	5.18	23781	3409	3408	0.413	100
2.33-2.4		0.307	0.361	5.63	23440	3328	3328	0.39	100
2.4-2.48		0.258	0.316	6.38	23027	3240	3238	0.341	99.9
2.48-2.57		0.201	0.258	7.59	22315	3134	3134	0.279	100
2.57-2.67		0.177	0.234	8.2	21510	2994	2994	0.253	100
2.67-2.78		0.153	0.189	9.62	21108	2930	2929	0.204	100
2.78-2.9		0.112	0.149	11.92	20153	2801	2798	0.161	99.9
2.9-3.04		0.085	0.125	13.93	19342	2692	2688	0.135	99.9
3.04-3.21		0.065	0.106	16.63	18244	2557	2552	0.114	99.8
3.21-3.4		0.05	0.086	19.7	17124	2398	2396	0.093	99.9
3.4-3.63		0.041	0.079	22	16280	2294	2291	0.085	99.9
3.63-3.93		0.037	0.067	24.16	14912	2117	2112	0.073	99.8
3.93-4.3		0.031	0.06	25.66	13900	1986	1982	0.065	99.8
4.3-4.81		0.027	0.056	27.33	12487	1777	1775	0.06	99.9
4.81-5.55		0.027	0.055	27.2	11198	1604	1603	0.06	99.9
5.55-6.8		0.026	0.053	26.6	9369	1354	1353	0.058	99.9
6.8-9.62		0.022	0.048	27.6	7245	1084	1083	0.052	99.9
	9.62	0.022	0.043	26.98	3371	632	548	0.047	86.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→19.573 Å / FOM work R set: 0.8147 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2236	2493	5.06 %
R_work	0.1823	46756	-
obs	0.1843	49249	99.78 %

Solvent computation

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

Displacement parameters

B_iso max: 143.73 Å² / B_iso mean: 51.96 Å² / B_iso min: 14.92 Å²

Refinement step

Cycle: final / Resolution: 2.15→19.573 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5245	0	3	236	5484
B_iso mean	-	-	54.58	44	-
Num. residues	-	-	-	-	663

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5339
X-RAY DIFFRACTION	f_angle_d	0.949	7207
X-RAY DIFFRACTION	f_chiral_restr	0.068	821
X-RAY DIFFRACTION	f_plane_restr	0.004	905
X-RAY DIFFRACTION	f_dihedral_angle_d	14.832	2039

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.1913	0.347	122	0.3065	2503	2625	98
2.1913-2.236	0.2696	134	0.2499	2560	2694	100
2.236-2.2845	0.2574	153	0.2196	2543	2696	100
2.2845-2.3376	0.2688	121	0.2126	2593	2714	100
2.3376-2.3959	0.2583	136	0.2055	2572	2708	100
2.3959-2.4606	0.2783	161	0.2052	2568	2729	100
2.4606-2.5329	0.2383	124	0.1963	2582	2706	100
2.5329-2.6144	0.2371	134	0.1959	2576	2710	100
2.6144-2.7077	0.2521	135	0.1993	2595	2730	100
2.7077-2.8158	0.2213	140	0.1886	2575	2715	100
2.8158-2.9435	0.273	129	0.2017	2603	2732	100
2.9435-3.0981	0.2597	143	0.1988	2582	2725	100
3.0981-3.2914	0.2739	139	0.2044	2608	2747	100
3.2914-3.5441	0.2105	148	0.1854	2595	2743	100
3.5441-3.8982	0.1974	135	0.1667	2622	2757	100
3.8982-4.4565	0.1967	142	0.1545	2633	2775	100
4.4565-5.5929	0.1861	145	0.1492	2681	2826	100
5.5929-19.5735	0.1953	152	0.1689	2765	2917	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	3.815	1.7996	-0.5361	4.1867	0.6119	1.8423	-0.0104	0.0788	-0.251	-0.1071	-0.12	0.0079	0.0796	0.1398	0.0713	0.1241	0.038	0.0011	0.2058	0.0053	0.168	-17.4413	-26.0234	5.1781
2	8.5319	2.7137	0.9892	3.029	1.5531	1.5971	-0.2246	0.1314	-1.1239	-0.093	0.2487	-0.5808	0.5021	0.2272	0.0144	0.3019	0.0457	0.0558	0.3284	-0.0704	0.3096	-10.5666	-32.5585	0.996
3	3.0774	0.7371	0.6005	3.7611	-0.2647	2.2254	-0.2705	-0.8221	-0.8403	0.4652	-0.0203	-0.6336	0.4675	0.3049	0.2812	0.3206	0.0828	0.0027	0.5349	0.1731	0.51	-0.5185	-29.7555	13.9666
4	3.8142	0.91	0.1041	2.6765	1.2766	1.569	-0.0309	0.6097	0.0501	-0.2026	-0.0002	0.3808	0.0522	-0.1311	0.0129	0.1625	0.0058	-0.0206	0.2495	0.024	0.2186	-27.03	-25.4225	1.5006
5	5.0911	1.6265	0.8464	2.6916	0.0705	0.8494	0.0566	0.4023	-0.5442	0.3579	0.0682	0.2751	0.1896	0.0873	0.0447	0.1228	-0.0011	0.0304	0.2032	-0.0513	0.3247	-33.8026	-31.0983	8.61
6	2.405	0.9411	-0.5373	3.8604	0.4539	2.7579	0.15	-0.2908	-0.0818	0.904	-0.1868	0.3723	0.2519	-0.2281	-0.0449	0.3635	0.0089	0.2078	0.2469	0.0219	0.4531	-43.5488	-24.493	30.8024
7	1.4027	-0.2068	-0.2797	5.456	0.0075	1.7318	-0.0218	-0.2276	-0.2839	1.016	-0.0469	-0.4647	-0.0374	0.101	-0.0543	0.5373	-0.0513	0.1071	0.2705	0.0455	0.7	-41.1356	-38.5964	30.5756
8	7.1077	1.9149	0.9273	4.4299	4.0751	7.5113	-0.2737	-1.1137	0.544	1.492	-0.0526	-0.3487	0.5758	0.7082	0.0693	0.776	-0.0113	-0.0164	0.3688	0.0889	0.9049	-36.4871	-44.9085	36.7041
9	1.2557	1.1809	0.6528	1.4482	-0.0799	1.378	-0.086	-0.3638	-0.268	1.0767	0.0295	0.3987	-0.0239	-0.037	0.101	0.4738	-0.0055	0.2206	0.2525	0.0227	0.4909	-43.0223	-21.5111	30.1167
10	5.4974	-3.3174	-0.4945	2.0996	0.5907	2.258	0.0789	-0.0542	0.1729	-0.0035	-0.094	0.8146	-0.7381	-0.0047	0.0567	0.3095	0.0552	0.1157	0.1095	-0.0388	0.7511	-46.8483	-13.113	21.5591
11	1.3806	-0.9922	-0.75	2.3408	0.8539	1.3553	-0.1109	-0.0763	0.0396	0.398	0.0875	0.453	-0.0704	-0.0956	0.0158	0.3157	0.0165	0.1317	0.1641	0.0274	0.3942	-42.0929	-10.846	27.6647
12	6.0891	-0.4743	-4.6624	3.2535	1.9246	6.6652	0.0609	-0.1782	0.0376	0.3171	0.0913	-0.3953	0.0137	0.4913	-0.2243	0.3193	-0.0408	-0.0665	0.3571	-0.1222	0.4421	-13.0279	-3.5247	25.709
13	4.0585	0.4795	-2.2337	2.8627	0.8095	2.8375	0.405	-0.2317	0.4386	0.1621	-0.0785	0.2252	-0.3289	0.3361	-0.2757	0.3482	0.0084	0.0199	0.2152	-0.0437	0.2599	-21.7964	0.7367	29.6971
14	5.8978	1.9695	-1.5577	1.5304	-1.1481	0.8726	0.387	-0.1334	-0.0156	0.2462	0.117	-0.4164	-0.4292	0.5622	-0.3141	0.5006	-0.1422	-0.0438	0.6202	-0.287	0.5693	-8.533	3.9341	29.3617
15	6.6222	-1.4495	-0.7482	4.2998	-0.0124	4.7603	0.3743	-0.7482	0.2895	0.57	0.0155	-0.5003	0.1221	0.6178	-0.4395	0.6572	-0.0591	-0.0967	0.5395	-0.1516	0.3902	-18.0451	-0.6134	41.0304
16	2.8313	2.0711	0.5154	2.5017	-0.9174	3.5817	0.0074	-0.6668	-0.5247	1.3457	-0.175	-0.634	0.6749	1.1149	0.3207	0.909	0.2001	-0.1936	0.8332	-0.0038	0.4993	-14.0988	-7.9751	47.7337
17	3.3442	0.9961	-1.3645	2.2044	-0.0072	3.031	0.1998	0.1145	0.5586	0.1142	0.1774	-0.8973	-0.537	0.6142	-0.2251	0.2936	-0.0781	0.1055	0.3439	-0.1047	0.6418	-14.8442	1.3163	20.2194
18	3.9158	0.915	-0.9547	4.1512	1.2957	3.4631	-0.0227	0.0566	0.6205	0.1717	0.2504	0.1745	-0.5718	0.0388	-0.1936	0.2644	-0.0056	0.0494	0.1921	-0.0291	0.4136	-25.5042	0.1547	20.138
19	2.4032	-0.2053	-0.5011	4.6384	0.8051	2.4625	0.285	0.0986	0.6074	-0.5286	0.1122	-0.0952	-0.7257	0.2922	-0.2906	0.4139	-0.0564	0.1162	0.3054	-0.0143	0.561	-12.8613	-1.2125	11.9436

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 38 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 72 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 138 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 139 through 213 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 214 through 229 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 54 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 55 through 92 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 127 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 128 through 173 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 174 through 187 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 188 through 229 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 18 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 19 through 38 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 39 through 56 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 57 through 87 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 88 through 138 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 139 through 179 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 180 through 200 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 201 through 227 )	C

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