PDB-5unb: Crystal structure of putative Putative deoxyribonuclease-2 from B...

ID or keywords:

Entry

Database: PDB / ID: 5unb

Title

Crystal structure of putative Putative deoxyribonuclease-2 from Burkholderia thailandensis in complex with copper

Components

Putative deoxyribonuclease-2

Keywords

HYDROLASE / SSGCID / Putative deoxyribonuclease-2 / inhitition / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

deoxyribonuclease II activity / Deoxyribonuclease II / Deoxyribonuclease II / Hydrolases; Acting on ester bonds / COPPER (II) ION / Putative deoxyribonuclease-2

Function and homology information

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: Structure of acid deoxyribonuclease.
Authors: Varela-Ramirez, A. / Abendroth, J. / Mejia, A.A. / Phan, I.Q. / Lorimer, D.D. / Edwards, T.E. / Aguilera, R.J.

History

Deposition	Jan 30, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2017	Group: Database references
Revision 1.2	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 4, 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 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5unb.cif.gz	297.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5unb.ent.gz	238.3 KB	Display	PDB format
PDBx/mmJSON format	5unb.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/un/5unb ftp://data.pdbj.org/pub/pdb/validation_reports/un/5unb	HTTPS FTP

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Related structure data

Related structure data	5i3eSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5i3e-d 3uzd-2 1eai-d 2c63-2 3w0k-d 4e2e-2 6y6b-d 5ewz-d 6kxm-d 6gkg-3 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: ButhA.18065.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative deoxyribonuclease-2

B: Putative deoxyribonuclease-2

hetero molecules

79.9 kDa, 2 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)	51.550, 61.070, 104.470
Angle α, β, γ (deg.)	90.000, 90.290, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative deoxyribonuclease-2 / Deoxyribonuclease II Mass: 39774.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria) Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II0389 / Plasmid: ButhA.18065.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2T8B0, Hydrolases; Acting on ester bonds
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.07 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: JCSG+ H3 optimization screen, condition H3: 22.75% PEG 3350, 100mM BisTris pH 6.25: ButhA.18065.a.B1 at 26.5mg/ml: over night soak with 5mM CuSO4: cryo: 20% EG and 5mM CuSO4: tray 249901h3, puck dgx5-1.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 30, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.75→26.361 Å / Num. obs: 65444 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.411 % / B_iso Wilson estimate: 18.21 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / R_rim(I) all: 0.056 / Χ²: 0.977 / Net I/σ(I): 20.97

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.75-1.8	3.955	0.322	3.95	4675	4675	0.887	0.372	96.7
1.8-1.84	4.619	0.262	5.48		4721	0.938	0.296	99.9
1.84-1.9	5.06	0.209	7.26		4561	0.966	0.233	100
1.9-1.96	5.641	0.166	9.62		4440	0.983	0.183	100
1.96-2.02	5.686	0.13	12.17		4282	0.99	0.143	100
2.02-2.09	5.689	0.104	14.92		4207	0.993	0.114	100
2.09-2.17	5.7	0.087	17.19		4026	0.994	0.096	100
2.17-2.26	5.683	0.074	19.68		3879	0.996	0.081	100
2.26-2.36	5.7	0.068	21.26		3726	0.996	0.075	100
2.36-2.47	5.704	0.062	23.29		3560	0.997	0.068	99.9
2.47-2.61	5.685	0.056	25.53		3366	0.997	0.062	100
2.61-2.77	5.685	0.048	28.8		3233	0.998	0.053	99.9
2.77-2.96	5.663	0.042	31.76		2995	0.998	0.047	100
2.96-3.2	5.639	0.038	35.67		2846	0.999	0.042	100
3.2-3.5	5.636	0.035	38.97		2574	0.998	0.039	100
3.5-3.91	5.622	0.034	41.67		2351	0.999	0.038	99.9
3.91-4.52	5.598	0.034	42.93		2081	0.999	0.037	100
4.52-5.53	5.541	0.034	43.3		1777	0.998	0.037	99.9
5.53-7.83	5.428	0.039	42.1		1377	0.998	0.043	99.6
7.83-50	4.764	0.044	40.7		767	0.997	0.049	96.4

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2650: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: native structure, 5i3e

5i3e

Resolution: 1.75→26 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.11

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1805	3334	5.1 %	0
R_work	0.1476	-	-	-
obs	0.1493	65407	99.67 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 98.02 Å² / B_iso mean: 24.0287 Å² / B_iso min: 8.27 Å²

Refinement step

Cycle: final / Resolution: 1.75→26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5267	0	11	742	6020
B_iso mean	-	-	30.35	32.62	-
Num. residues	-	-	-	-	681

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5498
X-RAY DIFFRACTION	f_angle_d	0.882	7516
X-RAY DIFFRACTION	f_chiral_restr	0.058	816
X-RAY DIFFRACTION	f_plane_restr	0.005	967
X-RAY DIFFRACTION	f_dihedral_angle_d	11.45	3251

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.75-1.775	0.2234	139	0.1835	2446	2585	95
1.775-1.8015	0.2399	146	0.1756	2529	2675	99
1.8015-1.8296	0.1987	133	0.1669	2594	2727	100
1.8296-1.8596	0.1959	139	0.1616	2578	2717	100
1.8596-1.8917	0.2095	152	0.1677	2564	2716	100
1.8917-1.9261	0.2169	128	0.1621	2562	2690	100
1.9261-1.9631	0.1866	142	0.1492	2609	2751	100
1.9631-2.0032	0.21	135	0.1528	2578	2713	100
2.0032-2.0467	0.1959	137	0.1456	2604	2741	100
2.0467-2.0943	0.1993	131	0.1447	2579	2710	100
2.0943-2.1467	0.1794	138	0.1445	2582	2720	100
2.1467-2.2047	0.1791	152	0.1426	2539	2691	100
2.2047-2.2695	0.1795	137	0.144	2616	2753	100
2.2695-2.3427	0.2159	141	0.1463	2613	2754	100
2.3427-2.4264	0.1738	133	0.1496	2559	2692	100
2.4264-2.5235	0.1942	153	0.1501	2583	2736	100
2.5235-2.6382	0.187	126	0.1543	2604	2730	100
2.6382-2.7772	0.214	150	0.1531	2596	2746	100
2.7772-2.951	0.1856	124	0.1591	2601	2725	100
2.951-3.1785	0.162	138	0.1488	2613	2751	100
3.1785-3.4977	0.1549	143	0.1398	2601	2744	100
3.4977-4.0023	0.1563	131	0.128	2642	2773	100
4.0023-5.0367	0.1385	148	0.1214	2619	2767	100
5.0367-26.3642	0.1945	138	0.1715	2662	2800	99

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	1.8895	-0.1626	0.3755	0.1236	0.3029	1.6378	-0.2548	0.7084	0.0766	-0.5322	0.2325	-0.0159	-0.3154	0.0127	0.0328	0.2867	-0.0084	-0.0137	0.3301	0.0116	0.0849	13.8141	7.5746	54.5192
2	1.3318	0.9413	0.1528	1.0847	0.142	1.1564	-0.2334	0.569	0.0329	-0.3323	0.1851	0.0487	-0.055	-0.0239	0.0502	0.2787	0.0003	-0.039	0.3507	0.0041	0.1223	9.1375	6.9103	53.3127
3	2.8694	0.2471	-0.7669	2.7836	0.1585	2.6229	-0.0423	0.1357	0.2428	-0.103	0.0298	0.2729	-0.1506	-0.2123	0.0818	0.1458	0.0491	-0.0259	0.2339	-0.0563	0.1899	-1.9754	7.7163	72.2861
4	2.5564	0.8792	0.5075	1.2104	0.1351	0.9411	-0.1173	0.4798	0.1687	-0.3045	0.0451	0.2475	-0.1217	-0.2084	0.1028	0.1921	0.0158	-0.0492	0.2762	-0.0277	0.1092	2.8647	5.4026	60.1333
5	1.384	0.481	0.2355	1.2973	0.1944	1.1531	-0.0768	0.2819	-0.202	-0.1437	-0.0112	0.2476	0.145	-0.2726	0.0576	0.1652	-0.0062	-0.0332	0.2518	-0.0884	0.2043	-2.8975	-4.6129	63.4329
6	2.5386	-1.3682	1.5824	1.3346	-0.9547	0.9574	-0.0803	-0.3602	-0.5957	0.1249	0.0982	0.3708	0.1941	-0.336	0.0427	0.2085	-0.0515	0.006	0.2491	-0.0451	0.291	0.2158	-11.087	72.2626
7	1.4677	0.5955	0.321	0.8473	0.4638	0.4415	-0.0076	0.156	-0.1514	-0.1083	0.0549	-0.1231	-0.0017	0.0412	-0.0563	0.1082	0.0343	0.0099	0.1216	-0.0162	0.105	21.976	2.9737	72.8521
8	1.848	0.6733	0.6758	1.4412	0.3266	1.7388	0.055	0.1093	-0.3148	-0.0788	-0.0088	-0.2398	0.0886	-0.044	0.0338	0.12	0.0334	0.0007	0.141	-0.0355	0.1567	15.7368	-4.4902	70.6107
9	2.1897	0.7013	1.0884	0.8641	0.5443	0.7345	0.0392	0.2079	-0.2215	0.0154	0.1516	-0.1914	0.104	0.1519	-0.1931	0.1268	0.0297	0.0109	0.1823	-0.0453	0.1919	31.8473	3.1326	73.0498
10	1.9998	2.0001	1.9999	2	-1.5878	2.0001	-1.4009	1.8168	-0.4659	-6.2296	0.7692	5.7523	1.3185	-1.4463	0.5934	1.2996	-0.4961	0.4179	1.0862	0.2961	0.8055	22.4077	0.3002	89.4608
11	1.538	-0.4841	-0.727	0.7768	0.6654	2.034	0.0028	-0.1258	-0.0147	0.0619	0.0304	-0.0357	0.0881	0.1551	-0.0436	0.0764	0.0033	-0.0114	0.0704	0.0135	0.0929	24.8564	24.6283	103.8301
12	3.2688	0.9314	0.1952	1.4178	-0.0495	0.2657	0.0105	-0.0927	-0.397	-0.0052	0.0907	0.1498	0.1431	-0.1281	-0.0853	0.1528	-0.0072	0.003	0.1086	0.0279	0.1947	7.7059	19.6834	107.0969
13	1.9911	0.5487	-0.2686	1.1379	-0.0563	1.2086	0.0217	-0.0728	-0.2452	0.066	-0.0506	0.1766	0.1403	-0.1259	0.0062	0.1204	-0.0145	0.0041	0.0877	0.0172	0.1772	5.0521	23.688	105.1884
14	1.0079	-0.0526	-0.3021	0.9797	-0.4593	2.1089	0.0283	0.1799	-0.0233	-0.1577	-0.0089	0.223	0.0702	-0.4296	-0.0987	0.115	0.0069	-0.0234	0.1732	0.0031	0.1967	0.4373	32.6636	95.765
15	1.211	-0.0151	-0.574	1.3573	0.9801	1.6648	0.0416	0.1826	0.0298	-0.2613	0.0044	-0.0548	-0.1382	0.0192	-0.0656	0.1745	0.0153	0.0172	0.1285	0.0219	0.1102	22.4995	27.5816	76.9345
16	1.1842	-0.1602	-0.2935	1.0046	0.5427	1.2795	0.0308	0.077	0.0312	-0.0854	-0.0322	0.0584	-0.0123	-0.0552	-0.0154	0.1049	0.0072	-0.009	0.0652	0.0183	0.1022	16.8035	30.4187	90.4432
17	1.1112	-0.5309	-0.7759	1.5438	1.2612	4.5799	0.0547	0.1866	0.1047	-0.3359	0.0014	-0.0616	-0.1802	0.1439	-0.0832	0.1961	-0.0012	0.0267	0.0909	0.0378	0.1272	23.9768	33.8653	79.8057

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 30 )	A	1 - 30
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 82 )	A	31 - 82
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 102 )	A	83 - 102
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 138 )	A	103 - 138
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 139 through 184 )	A	139 - 184
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 185 through 201 )	A	185 - 201
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 202 through 284 )	A	202 - 284
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 285 through 314 )	A	285 - 314
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 315 through 347 )	A	315 - 347
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 348 through 348 )	A	348
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 60 )	B	1 - 60
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 61 through 108 )	B	61 - 108
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 109 through 178 )	B	109 - 178
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 179 through 230 )	B	179 - 230
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 231 through 263 )	B	231 - 263
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 264 through 314 )	B	264 - 314
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 315 through 348 )	B	315 - 348

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi