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

ID or keywords:

Entry

Database: PDB / ID: 4you

Title

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 2.20A 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 / Alpha Beta / 3-5 exonuclease PhoExo I

Function and homology information

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 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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PDBx/mmCIF format	4you.cif.gz	261.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4you.ent.gz	213.5 KB	Display	PDB format
PDBx/mmJSON format	4you.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4yorC 4yotC 4yovC 4yowC 4yoxC 4yoyC 4yoz C: citing same article (ref.)
Similar structure data	4yoy-d 4o8u-1 4yor-1 4yow-d 4yov-d 4yox-d 5chi-d 4o8u-2 4yor-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: 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)	81.940, 88.980, 93.950
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.: 97 / 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: 2.22 Å³/Da / Density % sol: 44.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: CaCl2, Bis-Tris, 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: 2.2→20 Å / Num. obs: 35388 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 34.2 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.067 / R_rim(I) all: 0.074 / Χ²: 0.976 / Net I/σ(I): 18.28 / Num. measured all: 196045

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
2.2-2.26		0.76	0.546	2.01	7964	2593	2530	0.639	97.6
2.26-2.32		0.825	0.496	2.53	9300	2528	2517	0.574	99.6
2.32-2.39		0.834	0.468	3.13	11000	2443	2440	0.53	99.9
2.39-2.46		0.904	0.415	4.08	13186	2388	2386	0.46	99.9
2.46-2.54		0.929	0.36	5.1	14471	2345	2345	0.393	100
2.54-2.63		0.952	0.309	5.94	13848	2233	2233	0.338	100
2.63-2.73		0.969	0.265	6.95	13403	2158	2158	0.29	100
2.73-2.84		0.981	0.193	9.53	12984	2104	2104	0.211	100
2.84-2.97		0.989	0.149	12.25	12418	2004	2003	0.163	100
2.97-3.11		0.993	0.114	15.76	11862	1922	1922	0.124	100
3.11-3.28		0.995	0.09	19.87	11376	1844	1843	0.098	99.9
3.28-3.48		0.997	0.065	26.05	10637	1742	1741	0.071	99.9
3.48-3.72		0.999	0.046	34.14	9974	1640	1639	0.051	99.9
3.72-4.02		0.999	0.038	39.69	9167	1526	1525	0.042	99.9
4.02-4.4		0.999	0.031	47.06	8361	1411	1408	0.034	99.8
4.4-4.92		0.999	0.026	51.63	7587	1295	1293	0.029	99.8
4.92-5.68		0.999	0.029	47.94	6757	1150	1148	0.032	99.8
5.68-6.96		0.999	0.03	46.92	5652	989	985	0.033	99.6
6.96-9.84		0.999	0.024	59.87	4234	780	775	0.026	99.4
	9.84	0.999	0.024	60.82	1864	461	393	0.026	85.2

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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

Resolution: 2.2→19.963 Å / FOM work R set: 0.848 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2329	1772	5.01 %
R_work	0.1933	33614	-
obs	0.1953	35386	99.7 %

Solvent computation

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

Displacement parameters

B_iso max: 117.51 Å² / B_iso mean: 45.26 Å² / B_iso min: 16.94 Å²

Refinement step

Cycle: final / Resolution: 2.2→19.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4972	0	3	97	5072
B_iso mean	-	-	50.89	41.56	-
Num. residues	-	-	-	-	630

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5061
X-RAY DIFFRACTION	f_angle_d	0.891	6838
X-RAY DIFFRACTION	f_chiral_restr	0.063	786
X-RAY DIFFRACTION	f_plane_restr	0.004	857
X-RAY DIFFRACTION	f_dihedral_angle_d	13.719	1921

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2-2.2594	0.2799	135	0.2514	2496	2631	98
2.2594-2.3258	0.2858	145	0.238	2530	2675	100
2.3258-2.4008	0.277	124	0.2189	2587	2711	100
2.4008-2.4864	0.2782	131	0.2021	2557	2688	100
2.4864-2.5858	0.2204	125	0.2037	2545	2670	100
2.5858-2.7032	0.2908	146	0.2084	2575	2721	100
2.7032-2.8453	0.2656	133	0.1999	2565	2698	100
2.8453-3.023	0.2521	144	0.2011	2584	2728	100
3.023-3.2555	0.2508	125	0.2033	2593	2718	100
3.2555-3.5814	0.2394	139	0.1859	2592	2731	100
3.5814-4.0958	0.204	123	0.1699	2630	2753	100
4.0958-5.1456	0.1832	158	0.1589	2614	2772	100
5.1456-19.9636	0.2314	144	0.2067	2746	2890	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	1.7295	0.8414	-1.2217	1.3971	0.2855	2.9481	0.0868	-0.2734	0.0287	0.0889	0.0101	-0.1392	-0.2343	0.7271	-0.0491	0.278	-0.0434	-0.0102	0.3623	-0.0029	0.1763	26.4346	85.0681	71.2315
2	2.4411	-0.3502	0.2249	2.8735	-0.1028	3.3604	-0.1081	-0.0036	0.0561	0.3185	0.0491	-0.4405	0.2855	0.7279	0.0379	0.3625	0.0087	-0.0817	0.421	-0.0178	0.224	27.653	81.028	85.642
3	2.5109	-0.3213	-0.8331	1.2774	-0.4701	1.5726	0.1386	-0.34	0.1301	0.0964	-0.1026	-0.6401	-0.1419	1.1829	0.0466	0.4044	0.0519	-0.0197	0.7069	-0.0125	0.3014	32.5785	80.5558	90.2046
4	0.3491	-0.3275	-0.842	0.9786	0.3717	2.5228	0.0128	0.0402	0.0454	0.0857	0.0333	-0.1031	-0.1451	0.138	-0.0402	0.2263	-0.04	-0.0379	0.2624	0.0089	0.167	20.8662	83.9218	66.783
5	1.6957	-0.9519	0.0995	3.391	-0.2622	2.0249	0.0531	0.0937	0.0058	0.1497	-0.0397	0.2337	-0.2804	0.412	0.0037	0.2582	-0.0806	0.0303	0.2945	0.0232	0.1898	26.7552	85.0521	54.0051
6	2.0072	0.5328	-0.6673	2.1471	0.6113	1.0628	0.0425	-0.2449	-0.551	0.5161	-0.1312	-0.0493	-0.0002	-0.1249	0.0602	0.3905	0.0098	-0.0084	0.2058	0.0716	0.3495	2.6394	56.1828	75.9429
7	2.4867	0.5289	0.3338	1.5209	-0.542	1.9996	0.0194	-0.2799	-0.5036	0.4907	-0.1447	-0.4841	-0.207	0.3996	0.1505	0.5052	-0.0061	0.0495	0.3511	0.1297	0.6748	8.6449	42.7793	73.6809
8	1.8262	0.0703	-0.4109	3.171	-0.9404	2.6969	0.0787	-0.4454	-0.0795	0.8254	-0.3204	-0.8693	0.126	0.1629	0.1398	0.3843	-0.0254	-0.044	0.2995	0.0653	0.4513	11.5766	38.8097	74.3761
9	1.1336	0.6156	-0.1452	2.9035	0.7022	1.1883	0.0663	-0.2498	-0.0138	0.289	-0.0826	0.4022	0.1426	-0.0563	-0.0014	0.225	-0.0308	0.065	0.2037	-0.0065	0.304	0.1813	66.4886	73.5561
10	2.5707	0.9643	-0.8927	2.489	-0.193	1.4747	0.039	-0.1747	-0.4321	0.3571	-0.2823	0.1402	0.3995	-0.031	0.2219	0.3249	0.005	0.1758	0.3466	-0.0794	0.4387	23.5953	53.8082	51.1395
11	1.4401	-0.0671	0.0395	1.2557	0.967	1.8962	-0.1833	0.2142	-0.6602	-0.0633	0.112	-0.0802	0.3818	0.2605	0.0745	0.3008	0.0343	0.1254	0.343	-0.074	0.4338	30.5874	55.8151	45.3837
12	2.7784	-0.2837	0.0716	2.0847	0.422	1.2475	-0.2445	-0.1327	-0.4081	0.4441	0.425	-0.3136	0.1116	0.0924	-0.1558	0.3911	0.1207	0.0078	0.4744	-0.0246	0.4435	42.4739	58.6052	54.6933
13	1.8948	0.3386	-0.9845	1.3128	0.0619	0.5035	-0.1317	0.3093	-0.3229	-0.133	-0.0364	0.0712	0.1749	-0.1576	0.1467	0.284	0.0051	0.0376	0.37	-0.1151	0.3999	15.1742	57.7763	47.2353

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 54 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 104 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 127 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 200 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 229 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 57 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 58 through 111 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 112 through 138 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 139 through 228 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 18 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 19 through 72 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 73 through 138 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 139 through 226 )	C

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