PDB-5i3e: Crystal structure of putative Putative deoxyribonuclease-2 from B...

ID or keywords:

Entry

Database: PDB / ID: 5i3e

Title

Crystal structure of putative Putative deoxyribonuclease-2 from Burkholderia thailandensis, E264

Components

Putative deoxyribonuclease-2

Keywords

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

Function / homology

deoxyribonuclease II activity / Deoxyribonuclease II / Deoxyribonuclease II / Hydrolases; Acting on ester bonds / Putative deoxyribonuclease-2

Function and homology information

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 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	Feb 10, 2016	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	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4	Jul 17, 2019	Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5	Mar 6, 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	5i3e.cif.gz	297.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/5i3e ftp://data.pdbj.org/pub/pdb/validation_reports/i3/5i3e	HTTPS FTP

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Related structure data

Related structure data	5unbC C: citing same article (ref.)
Similar structure data	2hjr-6 5unb-d 6rl3-1 6slx-1 6s9q-1 6rm5-1 5oeh-1 6yq2-1 6gkf-1 5ewz-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
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

79.7 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)	51.160, 61.750, 102.600
Angle α, β, γ (deg.)	90.000, 92.120, 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 / Fragment: ButhA.18065.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.04 Å³/Da / Density % sol: 39.58 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MCSG1 screen, b12: 100mM BisTris pH 6.5, 28% PEG MME 2000, trays set up at 26.5mg/ml, cryo: 15% EG; for phasing a crystal from 25% PEG 3350, 100mM BisTris pH 6.0 was incubated for 30s in a ...Details: MCSG1 screen, b12: 100mM BisTris pH 6.5, 28% PEG MME 2000, trays set up at 26.5mg/ml, cryo: 15% EG; for phasing a crystal from 25% PEG 3350, 100mM BisTris pH 6.0 was incubated for 30s in a buffer containing 15% EG and 750mM NaI, iodide data were collected at the in-house source; ButhA.18065.a.B1.PS18111 at 26.5 mg/ml

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.58 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 screen, b12: 100mM BisTris pH 6.5, 28% PEG MME 2000, trays set up at 26.5mg/ml, cryo: 15% EG; for phasing a crystal from 25% PEG 3350, 100mM BisTris pH 6.0 was incubated for 30s in a ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.2.2		1	0.999995
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Sep 25, 2013
RIGAKU SATURN 944+	2	CCD	Oct 25, 2013

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double crystal, Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Rigaku Varimax	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.999995	1
2	1.5418	1

Reflection

Resolution: 1.65→50 Å / Num. obs: 76021 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / B_iso Wilson estimate: 12.12 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.052 / Net I/σ(I): 16.74

Reflection shell

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.65-1.69		2.5	0.523	2.12	1	99.5
1.69-1.74			0.401	2.69	1	99.4
1.74-1.79			0.309	3.51	1	99.5
1.79-1.84			0.239	4.55	1	99.5
1.84-1.91			0.173	6.1	1	99.5
1.91-1.97			0.138	7.76	1	99.3
1.97-2.05			0.102	10.15	1	99.5
2.05-2.13			0.082	12.38	1	98.9
2.13-2.22			0.063	15.12	1	99.1
2.22-2.33			0.055	17.46	1	98.9
2.33-2.46			0.048	19.29	1	99
2.46-2.61			0.043	21.37	1	98.7
2.61-2.79			0.036	25.48	1	98.2
2.79-3.01			0.029	29.65	1	97.6
3.01-3.3			0.024	36.56	1	97.4
3.3-3.69			0.02	42.2	1	97.1
3.69-4.26			0.018	46.37	1	96.2
4.26-5.22			0.015	50.69	1	97.2
5.22-7.38			0.016	48.61	1	96.1
	7.38		0.014	53.41	1	93.4

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Processing

Software

Name	Classification
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
ARP	model building
REFMAC	refinement
XDS	data scaling
Coot	model building

Refinement

Method to determine structure:

SAD / Resolution: 1.65→39.443 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.14

	R_factor	Num. reflection	% reflection
R_free	0.1866	3745	4.93 %
R_work	0.1541	-	-
obs	0.1557	76000	98.7 %

Solvent computation

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

Displacement parameters

B_iso max: 69.43 Å² / B_iso mean: 19.2921 Å² / B_iso min: 4.32 Å²

Refinement step

Cycle: final / Resolution: 1.65→39.443 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5379	0	8	739	6126
B_iso mean	-	-	19.33	29.67	-
Num. residues	-	-	-	-	694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5660
X-RAY DIFFRACTION	f_angle_d	0.886	7755
X-RAY DIFFRACTION	f_chiral_restr	0.058	843
X-RAY DIFFRACTION	f_plane_restr	0.005	1003
X-RAY DIFFRACTION	f_dihedral_angle_d	11.377	3386

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.6709	0.2665	143	0.2377	2697	X-RAY DIFFRACTION	99
1.6709-1.6929	0.2923	130	0.2332	2648	X-RAY DIFFRACTION	100
1.6929-1.7161	0.2663	142	0.2215	2711	X-RAY DIFFRACTION	100
1.7161-1.7406	0.2497	143	0.2119	2657	X-RAY DIFFRACTION	99
1.7406-1.7666	0.2503	133	0.1952	2707	X-RAY DIFFRACTION	99
1.7666-1.7942	0.2422	121	0.1893	2634	X-RAY DIFFRACTION	99
1.7942-1.8236	0.2205	138	0.1791	2765	X-RAY DIFFRACTION	99
1.8236-1.855	0.2232	130	0.1687	2632	X-RAY DIFFRACTION	100
1.855-1.8888	0.1965	151	0.1641	2685	X-RAY DIFFRACTION	99
1.8888-1.9251	0.2065	150	0.163	2683	X-RAY DIFFRACTION	99
1.9251-1.9644	0.2119	138	0.1647	2705	X-RAY DIFFRACTION	99
1.9644-2.0071	0.2088	132	0.1646	2666	X-RAY DIFFRACTION	99
2.0071-2.0538	0.1773	136	0.1531	2728	X-RAY DIFFRACTION	99
2.0538-2.1051	0.1797	137	0.1494	2626	X-RAY DIFFRACTION	99
2.1051-2.1621	0.1987	132	0.1495	2705	X-RAY DIFFRACTION	99
2.1621-2.2257	0.1939	143	0.1504	2700	X-RAY DIFFRACTION	99
2.2257-2.2975	0.2095	130	0.1464	2671	X-RAY DIFFRACTION	99
2.2975-2.3796	0.1891	140	0.1504	2674	X-RAY DIFFRACTION	99
2.3796-2.4749	0.1843	137	0.1525	2670	X-RAY DIFFRACTION	99
2.4749-2.5875	0.1824	157	0.1578	2692	X-RAY DIFFRACTION	99
2.5875-2.7239	0.1976	138	0.1494	2636	X-RAY DIFFRACTION	98
2.7239-2.8945	0.198	131	0.1584	2668	X-RAY DIFFRACTION	98
2.8945-3.1179	0.1751	126	0.1481	2666	X-RAY DIFFRACTION	97
3.1179-3.4315	0.1789	144	0.1345	2671	X-RAY DIFFRACTION	97
3.4315-3.9276	0.1357	137	0.1252	2639	X-RAY DIFFRACTION	97
3.9276-4.9469	0.131	152	0.1217	2650	X-RAY DIFFRACTION	97
4.9469-50	0.1724	154	0.152	2669	X-RAY DIFFRACTION	95

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	0.9341	0.4216	-0.1114	0.5107	0.0033	0.614	-0.1879	0.5199	0.0386	-0.1947	0.1453	0.0757	-0.1446	-0.0142	0.101	0.1968	-0.0626	-0.045	0.3173	-0.02	0.0797	9.0264	7.4029	52.3789
2	0.7449	0.4471	0.1169	1.0967	0.4466	0.8243	-0.1165	0.1418	0.1007	-0.1485	-0.0955	0.2884	-0.1374	-0.2214	0.1315	0.1142	0.0239	-0.0448	0.196	-0.0573	0.1396	-0.533	6.2538	63.4023
3	1.0012	0.3838	0.3161	0.743	0.5227	0.7402	0.0064	0.1602	-0.2924	0.0216	0.0644	-0.0958	0.0725	0.0363	-0.0406	0.0977	0.0199	-0.011	0.1137	-0.0476	0.1187	14.0851	-0.7177	69.1479
4	1.2512	-0.0398	-0.4034	1.2663	0.3878	1.5391	0.026	-0.1422	0.0443	0.1854	0.0491	-0.0236	-0.0116	0.1765	-0.0647	0.1011	0.0013	0.0068	0.0586	-0.0092	0.0558	21.7079	26.0464	101.1479
5	1.7788	0.502	0.2912	1.0122	0.2745	0.7669	0.0134	-0.0779	-0.0827	0.1483	0.0012	0.2323	0.0966	-0.0399	-0.0065	0.1417	0.005	0.0379	0.063	0.0317	0.1424	6.8463	17.5736	102.2826
6	1.7311	-0.1412	-1.2281	0.4394	0.0416	1.657	-0.0731	-0.2406	-0.1701	0.2323	0.0227	0.2146	0.1315	0.0759	0.0078	0.1468	0	0.0549	0.0822	0.0151	0.1504	7.8709	20.1314	102.2394
7	0.681	0.1275	-0.1157	0.7986	0.0399	0.581	0.0026	0.0546	0.079	0.0263	0.0367	0.2556	-0.0084	-0.0828	-0.032	0.0818	0.0005	-0.0006	0.0509	0.0176	0.1493	6.8658	28.7066	90.0341
8	1.2702	-0.0872	-0.2955	1.1372	0.0442	0.8789	-0.0058	0.1531	0.0982	-0.1599	0.0556	0.1148	-0.0637	-0.0292	-0.0315	0.1073	-0.0107	-0.011	0.0497	0.0317	0.1113	15.2431	33.7632	82.584

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 82 )	A	1 - 82
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 138 )	A	83 - 138
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 139 through 348 )	A	139 - 348
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 51 )	B	1 - 51
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 52 through 102 )	B	52 - 102
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 103 through 138 )	B	103 - 138
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 139 through 284 )	B	139 - 284
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 285 through 348 )	B	285 - 348

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