PDB-3w2y: Crystal structure of DNA uridine endonuclease Mth212 mutant W205S

ID or keywords:

Entry

Database: PDB / ID: 3w2y

Title

Crystal structure of DNA uridine endonuclease Mth212 mutant W205S

Components

Exodeoxyribonuclease

Keywords

HYDROLASE / alpha/beta-sandwich / DNA binding

Function / homology

Function and homology information

exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Tabata, N. / Shida, T. / Arai, R.

Citation

Journal: To be Published
Title: Crystal structure of DNA uridine endonuclease Mth212
Authors: Tabata, N. / Shida, T. / Arai, R.

History

Deposition	Dec 6, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3w2y.cif.gz	237.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3w2y.ent.gz	194 KB	Display	PDB format
PDBx/mmJSON format	3w2y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3w2y_validation.pdf.gz	449.1 KB	Display	wwPDB validaton report
Full document	3w2y_full_validation.pdf.gz	450.5 KB	Display
Data in XML	3w2y_validation.xml.gz	24.1 KB	Display
Data in CIF	3w2y_validation.cif.gz	35.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w2/3w2y ftp://data.pdbj.org/pub/pdb/validation_reports/w2/3w2y	HTTPS FTP

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Related structure data

Related structure data	3w2xC 3fziS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3g1k-2 3g1k-1 2voa-3 6xxt-d 2jc4-d 6ql3-d 6sp5-1 3g0a-d 5y2y-1 6oe1-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (3) #19 - Jul 2001 Actin similarity (3) #91 - Jul 2007 Thymine Dimers similarity (1)

Deposited unit

A: Exodeoxyribonuclease

D: Exodeoxyribonuclease

hetero molecules

62.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Exodeoxyribonuclease

hetero molecules

defined by author&software
31.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Exodeoxyribonuclease

hetero molecules

defined by author&software
30.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.295, 100.295, 144.698
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Exodeoxyribonuclease Mass: 30572.684 Da / Num. of mol.: 2 / Mutation: W205S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH212, MTH_212 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26314, exodeoxyribonuclease III
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / 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: 3.44 Å³/Da / Density % sol: 64.2 % / Mosaicity: 0.53 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12.5% PEG3350, 50mM Magnesium formate dihydrate, 11.5mM uracil, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Dec 4, 2011

Radiation

Monochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 64714 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / R_merge(I) obs: 0.091 / Χ²: 1.019 / Net I/σ(I): 10.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.9-1.97	12	0.45	6.4	6465	1.02	100
1.97-2.05	12.1	0.29	9.9	6481	1.041	100
2.05-2.14	12.2	0.219	13	6455	1.037	100
2.14-2.25	12.3	0.185	15.5	6466	1.037	100
2.25-2.39	12.4	0.152	18.4	6471	1.012	100
2.39-2.58	12.5	0.124	22.2	6477	1.016	100
2.58-2.84	12.5	0.102	26.4	6475	1.038	100
2.84-3.25	12.5	0.08	31.4	6493	1.007	100
3.25-4.09	12.1	0.065	36	6495	0.995	99.9
4.09-50	11.1	0.06	33.2	6436	0.981	97.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.559 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1924	3265	5.1 %	RANDOM
R_work	0.1719	-	-	-
obs	0.173	64530	99.57 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 83.43 Å² / B_iso mean: 27.027 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.1 Å²	-0.05 Å²	0 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4258	0	59	381	4698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4477
X-RAY DIFFRACTION	r_angle_refined_deg	1.133	1.947	6007
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.148	5	521
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.132	22.798	243
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.06	15	772
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.304	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	598
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3483
X-RAY DIFFRACTION	r_mcbond_it	0.394	1.5	2579
X-RAY DIFFRACTION	r_mcangle_it	0.767	2	4167
X-RAY DIFFRACTION	r_scbond_it	1.384	3	1898
X-RAY DIFFRACTION	r_scangle_it	2.308	4.5	1840

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.258	233	-
R_work	0.214	4532	-
all	-	4765	-
obs	-	4765	99.75 %

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	2.273	0.9536	-0.3082	3.4672	0.2529	3.4071	-0.0443	0.0074	-0.1113	-0.1693	0.0335	-0.0941	0.0744	0.0724	0.0108	0.0543	0.0001	-0.0218	0.0429	-0.0119	0.0824	-9.714	20.635	-3.454
2	6.4134	0.0887	-2.3885	6.0412	-2.4815	7.9719	-0.0099	0.0303	-0.2287	-0.0223	0.1098	-0.2751	0.0858	0.3332	-0.0999	0.0719	0.0016	-0.0124	0.0874	-0.0469	0.1767	-4.258	14.636	-3.726
3	1.8952	1.2215	0.0607	3.3718	1.1164	1.7394	-0.161	0.261	-0.0601	-0.5403	0.2027	-0.0949	-0.1876	0.154	-0.0417	0.1367	-0.0353	-0.0173	0.1287	-0.0256	0.1277	-11.183	21.195	-11.507
4	6.9206	2.0135	-6.0486	2.8093	-2.0429	16.7521	-0.0273	0.5629	-0.2886	-0.4945	0.1782	-0.2337	-0.2426	0.0759	-0.151	0.2266	-0.0115	0.0453	0.1265	-0.0546	0.1885	-11.785	12.203	-13.113
5	3.0238	2.7895	0.0865	7.1303	0.5194	2.8174	-0.2051	0.2864	0.0766	-0.7206	0.203	-0.0983	-0.0986	0.0448	0.0021	0.1398	-0.0313	-0.0128	0.1382	-0.052	0.1123	-16.633	24.767	-14.84
6	1.8691	0.4175	0.2802	3.695	0.3547	1.285	-0.0999	0.1215	0.092	-0.2803	0.0071	0.0926	-0.2245	-0.0361	0.0928	0.143	0.0014	-0.0401	0.0793	-0.021	0.0788	-20.968	27.714	-9.975
7	3.6393	2.3309	0.1914	7.3619	0.7589	2.62	-0.1146	0.1432	0.0699	-0.2731	-0.0251	-0.0718	-0.2184	0.076	0.1396	0.0939	0.0303	-0.0546	0.0906	-0.0091	0.0462	-18.075	32.769	-3.242
8	6.3257	3.6072	-0.5565	4.519	-0.0018	2.7537	-0.1649	0.1941	0.4911	-0.3778	-0.009	0.2501	-0.4483	-0.0555	0.1739	0.1999	0.0333	-0.096	0.0659	0	0.1416	-20.107	42.488	-4.568
9	5.6003	1.6123	0.0985	2.5383	0.3185	0.7215	-0.0762	0.1444	-0.0004	-0.0684	-0.0924	0.296	-0.0892	-0.2034	0.1686	0.0938	0.0092	-0.0368	0.133	-0.0653	0.1029	-26.788	30.226	1.536
10	2.2957	-1.9277	0.3597	3.9585	-0.1053	3.4477	-0.0779	-0.0937	0.4902	0.1056	-0.0367	-0.275	-0.3303	0.1724	0.1146	0.1203	-0.0276	-0.0454	0.0673	-0.0399	0.1679	-6.711	41.981	10.459
11	1.8341	0.0558	0.42	1	0.3993	0.9156	-0.0211	-0.1199	0.1114	0.0135	-0.0498	0.1014	-0.1091	-0.0389	0.071	0.0907	-0.0103	-0.0237	0.0902	-0.0362	0.0815	-14.729	35.707	9.546
12	30.0779	3.4795	12.5406	0.2275	-3.4914	7.7993	-0.4972	3.2182	0.5252	-0.0477	0.1277	-0.148	-0.1125	1.6744	0.3695	0.221	-0.0892	0.0369	0.5543	0.0323	0.1788	6.474	34.15	0.986
13	3.9653	1.015	0.8723	1.4952	0.2819	0.8225	-0.0464	0.0127	0.0348	0.0177	-0.0508	-0.0014	-0.0473	0.0504	0.0972	0.0791	-0.0159	-0.0117	0.0524	-0.0136	0.0632	-9.973	31.23	7.122
14	4.8881	-0.1571	-1.1601	1.2662	0.644	3.0525	-0.0457	-0.2995	-0.3966	0.1178	-0.0846	0.0689	0.1762	0.0349	0.1303	0.0906	-0.0113	-0.0049	0.054	-0.0229	0.1068	-13.001	21.316	7.193
15	1.6932	-0.891	0.7244	3.505	1.6801	2.361	-0.132	-0.2813	0.1221	0.5633	-0.2103	0.3262	0.3547	-0.4885	0.3422	0.2276	-0.0159	0.0624	0.2466	-0.1591	0.2103	-29.823	44.172	26.262
16	3.9459	-5.6345	-1.0007	9.5246	4.5083	7.4906	-0.1986	-0.3815	-0.4415	1.2795	-0.5739	0.988	1.1792	-1.05	0.7725	0.6289	-0.3973	0.3049	0.6946	-0.323	0.4	-33.856	39.009	30.083
17	0.8846	-0.7529	-1.7045	3.95	2.4613	6.9266	-0.0552	-0.0382	0.1063	0.1115	-0.4167	0.5616	-0.0839	-0.7498	0.4719	0.133	0.0597	-0.0215	0.2757	-0.2075	0.3063	-31.246	47.873	20.565
18	9.082	0.4281	-1.8294	5.3523	5.8124	19.2104	-0.0947	0.0365	0.0559	0.1509	-0.997	1.1143	0.6103	-2.4959	1.0916	0.0669	-0.0527	0.0429	0.6265	-0.383	0.4686	-40.851	43.75	20.547
19	9.4657	-1.454	-11.5694	7.4475	2.57	25.4336	-0.0464	0.8904	0.0735	-1.088	-1.3244	0.921	-1.4483	-1.8099	1.3708	0.3151	0.3128	-0.3406	0.4627	-0.442	0.5255	-32.009	52.628	14.4
20	7.8109	-2.2969	-6.9499	4.2626	4.9227	13.3139	-0.3208	0.4922	0.0877	-0.2284	-0.2952	0.3852	-0.0933	-0.8355	0.616	0.1639	0.0438	-0.0778	0.2045	-0.1429	0.2461	-27.954	50.023	15.054
21	8.6663	1.1709	-0.0863	5.1023	0.5547	6.4983	-0.5863	-0.1766	1.1545	-0.2723	-0.2817	0.488	-0.8183	-0.9858	0.868	0.3141	0.2391	-0.2808	0.2922	-0.324	0.4604	-32.09	59.923	20.736
22	3.6077	-1.4148	-0.6561	3.1204	2.122	3.2649	-0.1889	-0.078	0.4902	-0.1801	-0.0324	-0.1067	-0.4323	-0.1686	0.2212	0.2571	0.0743	-0.1392	0.0887	-0.1153	0.298	-21.41	59.31	20.549
23	2.0303	-1.1085	1.2108	10.3733	0.4916	3.8449	-0.4709	-0.4298	0.5008	0.028	-0.1605	-0.2195	-0.7324	-0.5799	0.6314	0.3399	0.2381	-0.2685	0.2485	-0.3271	0.4572	-26.642	67.15	30.419
24	2.2864	-1.0553	0.2324	4.6331	1.4683	3.7724	-0.2147	-0.2121	0.5045	0.2041	0.4601	-0.6924	0.0763	0.5266	-0.2454	0.1404	0.0965	-0.16	0.1916	-0.2273	0.3375	-7.129	53.236	27.713
25	1.8087	-1.2387	-0.7511	6.6522	3.4679	1.7937	-0.373	-0.4554	0.3066	0.5477	0.4043	-0.2075	0.285	0.1577	-0.0312	0.3247	0.1563	-0.1324	0.2393	-0.1831	0.1953	-15.036	50.557	34.561
26	2.9306	-2.7879	-1.2927	5.3995	1.6647	2.584	-0.2608	-0.2419	0.2633	0.5719	0.1794	-0.3231	0.4965	0.0447	0.0814	0.3202	0.1174	-0.1153	0.1865	-0.1445	0.1638	-15.81	47.819	31.946
27	0.9722	-0.9142	0.3085	9.2589	5.6206	7.143	-0.3918	-0.3591	0.0574	1.4311	-0.1246	0.5684	0.86	-0.489	0.5165	0.4277	0.0776	0.0324	0.2675	-0.164	0.1548	-25.635	49.104	36.742

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 18
2	X-RAY DIFFRACTION	2	A	19 - 30
3	X-RAY DIFFRACTION	3	A	31 - 48
4	X-RAY DIFFRACTION	4	A	49 - 56
5	X-RAY DIFFRACTION	5	A	57 - 65
6	X-RAY DIFFRACTION	6	A	66 - 102
7	X-RAY DIFFRACTION	7	A	103 - 119
8	X-RAY DIFFRACTION	8	A	120 - 135
9	X-RAY DIFFRACTION	9	A	136 - 153
10	X-RAY DIFFRACTION	10	A	154 - 169
11	X-RAY DIFFRACTION	11	A	170 - 206
12	X-RAY DIFFRACTION	12	A	207 - 211
13	X-RAY DIFFRACTION	13	A	212 - 229
14	X-RAY DIFFRACTION	14	A	230 - 257
15	X-RAY DIFFRACTION	15	D	2 - 19
16	X-RAY DIFFRACTION	16	D	20 - 31
17	X-RAY DIFFRACTION	17	D	32 - 44
18	X-RAY DIFFRACTION	18	D	45 - 57
19	X-RAY DIFFRACTION	19	D	58 - 65
20	X-RAY DIFFRACTION	20	D	66 - 73
21	X-RAY DIFFRACTION	21	D	74 - 91
22	X-RAY DIFFRACTION	22	D	92 - 136
23	X-RAY DIFFRACTION	23	D	137 - 150
24	X-RAY DIFFRACTION	24	D	151 - 183
25	X-RAY DIFFRACTION	25	D	184 - 210
26	X-RAY DIFFRACTION	26	D	211 - 229
27	X-RAY DIFFRACTION	27	D	230 - 257

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