PDB-3teb: endonuclease/exonuclease/phosphatase family protein from Leptotri...

ID or keywords:

Entry

Database: PDB / ID: 3teb

Title

endonuclease/exonuclease/phosphatase family protein from Leptotrichia buccalis C-1013-b

Components

Endonuclease/exonuclease/phosphatase

Keywords

HYDROLASE / PSI-BIOLOGY / MCSG / Midwest center for structural genomics

Function / homology

Function and homology information

exonuclease activity /

endonuclease activity
Similarity search - Function

Biological species

Leptotrichia buccalis C-1013-b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.99 Å

Authors

Chang, C. / Bigelow, L. / Muniez, I. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of endonuclease/exonuclease/phosphatase family protein from Leptotrichia buccalis C-1013-b
Authors: Chang, C. / Bigelow, L. / Muniez, I. / Bearden, J. / Joachimiak, A.

History

Deposition	Aug 12, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3teb.cif.gz	225.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3teb.ent.gz	194.9 KB	Display	PDB format
PDBx/mmJSON format	3teb.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/te/3teb ftp://data.pdbj.org/pub/pdb/validation_reports/te/3teb	HTTPS FTP

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Related structure data

Similar structure data	2puj-d 5ysp-2 7atq-2 3pmb-2 5ncj-2 5ysq-2 6y9g-2 2pu7-d 6szp-d 7e4l-1 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
Other databases	TargetDB: APC101233

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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)

Deposited unit

A: Endonuclease/exonuclease/phosphatase

B: Endonuclease/exonuclease/phosphatase

hetero molecules

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

1

A: Endonuclease/exonuclease/phosphatase

hetero molecules

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

2

B: Endonuclease/exonuclease/phosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	206.915, 206.915, 89.271
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22

#1: Protein	Endonuclease/exonuclease/phosphatase Mass: 31321.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptotrichia buccalis C-1013-b (bacteria) Strain: ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / Gene: Lebu_1528 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7NB70
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 125 / 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: 4.4 Å³/Da / Density % sol: 72.07 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.5M Magnesium formate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2011
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97912 Å / Relative weight: 1
Reflection	Resolution: 2.99→50 Å / Num. all: 23185 / Num. obs: 23166 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 17.8 % / R_merge(I) obs: 0.104 / Net I/σ(I): 36.56
Reflection shell	Resolution: 3→3.03 Å / Redundancy: 18.2 % / R_merge(I) obs: 0.999 / Mean I/σ(I) obs: 5.17 / Num. unique all: 544 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
RESOLVE		phasing
ARP/wARP		model building
Coot		model building
CNS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.99→50 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.903 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 25.238 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.3
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2157	1166	5.2 %	RANDOM
R_work	0.1757	-	-	-
all	0.1778	22578	-	-
obs	0.1778	22578	97.56 %	-

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: 132.6 Å² / B_iso mean: 39.9018 Å² / B_iso min: 18.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.73 Å²	0.37 Å²	0 Å²
2-	-	0.73 Å²	0 Å²
3-	-	-	-1.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.99→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4266	0	2	125	4393

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4338
X-RAY DIFFRACTION	r_angle_refined_deg	1.287	1.933	5847
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.23	5	519
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.765	25.702	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.692	15	822
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.826	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	650
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3242
X-RAY DIFFRACTION	r_mcbond_it	1.429	1.5	2588
X-RAY DIFFRACTION	r_mcangle_it	2.671	2	4197
X-RAY DIFFRACTION	r_scbond_it	2.41	3	1750
X-RAY DIFFRACTION	r_scangle_it	4.269	4.5	1650
X-RAY DIFFRACTION	r_rigid_bond_restr	1.233	3	4338

LS refinement shell

Resolution: 2.992→3.069 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	69	-
R_work	0.236	1292	-
all	-	1361	-
obs	-	1361	86.47 %

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	0.247	-0.734	0.2525	0.623	-0.1521	0.8103	0.0911	0.0269	-0.0281	-0.1844	0.0374	0.0241	0.0162	0.0411	-0.1285	0.2245	0.007	-0.0116	0.1708	-0.0042	0.2753	57.889	42.632	7.86
2	2.136	0.2767	1.5841	7.7713	-1.6352	3.0565	0.0558	-0.1348	0.1565	-0.0063	0.034	-0.0283	-0.0939	0.1184	-0.0899	0.1507	0.0197	0.012	0.1687	0.0048	0.2298	70.073	51.519	19.515
3	-0.2925	-0.4589	0.2894	3.4722	1.6741	1.7038	0.0548	-0.027	0.1012	-0.3501	-0.0296	-0.0617	-0.1008	0.0063	-0.0253	0.2093	0.0217	-0.0011	0.1932	0.0068	0.2302	64.401	50.666	5.226
4	0.3893	0.3764	0.1872	-0.0768	0.4267	0.0904	-0.0117	-0.031	-0.006	-0.0408	0.0139	0.0496	-0.0094	-0.0059	-0.0022	0.188	0.0343	0.0093	0.1718	-0.0091	0.2565	56.215	54.172	19.5
5	0.4858	-0.2824	1.5394	1.575	-1.4082	3.4199	0.0817	0.1028	0.0355	-0.2609	-0.1397	0.0133	0.1815	0.1756	0.058	0.1934	0.0584	0.0031	0.1696	0.0142	0.2593	52.175	56.048	17.415
6	-0.0764	0.1241	0.2166	-2.0528	1.9948	-0.4021	0.0036	0.0442	0.0353	-0.0165	0.1456	0.1958	0.0649	-0.2478	-0.1492	0.2426	0.0433	-0.0016	0.2163	0.0402	0.3343	44.965	51.586	20.818
7	0.8189	-0.1583	0.4495	1.1773	0.1486	0.7206	-0.073	-0.0337	0.0216	-0.0311	0.0643	0.1471	0.0152	-0.0894	0.0087	0.1813	0.0213	-0.0222	0.1786	0.0031	0.2965	39.108	51.621	17.041
8	4.0962	-0.7599	4.5809	3.7456	-4.425	7.5794	0.3688	0.1408	-0.4526	-0.0707	0.113	0.4234	0.3044	0.058	-0.4818	0.168	0.044	-0.083	0.1741	-0.0066	0.3646	40.801	34.869	9.317
9	1.9934	-1.3444	1.6393	0.1512	-0.5157	0.2685	-0.1018	0.0549	0.1799	-0.1601	0.0411	0.0783	-0.0192	-0.0336	0.0607	0.2797	0.0354	-0.0827	0.1468	0.0676	0.3386	41.648	44.741	7.412
10	1.3561	-0.3773	1.536	3.0966	-1.8384	1.3837	-0.0154	0.1116	-0.1082	-0.2012	-0.0098	0.2555	0.2161	0.0192	0.0252	0.2011	0.0118	-0.0753	0.1711	-0.0197	0.3336	49.104	40.656	4.651
11	0.7002	0.1898	0.0871	0.182	-0.152	1.1394	-0.0232	-0.1346	-0.0236	0.015	0.1222	-0.1343	0.1113	0.3209	-0.099	0.1676	0.0122	-0.0153	0.2547	-0.0418	0.2868	72.829	66.584	45.812
12	1.7772	3.5466	-3.0503	6.058	-1.6673	10.4796	0.0029	-0.0339	0.1095	-0.1306	0.0251	-0.0542	-0.0067	0.1771	-0.028	0.1361	0.0525	0.014	0.1695	-0.0054	0.2792	72.605	53.129	32.669
13	0.7756	0.5287	1.5691	0.7195	0.247	4.1311	0.0711	-0.1398	-0.1683	0.1247	0.0004	0.0371	0.3456	0.2796	-0.0715	0.1623	0.0474	0.0043	0.2422	-0.0098	0.2659	72.828	56.09	47.77
14	0.0427	-0.2807	-0.3435	0.3248	-0.108	1.2142	0.0597	-0.1018	0.042	-0.0031	0.0098	-0.0213	-0.0271	0.1324	-0.0696	0.1733	0.0008	-0.0069	0.1904	-0.0228	0.2544	61.37	60.682	36.006
15	0.2211	0.0448	0.0641	1.3409	-1.0927	2.9386	0.0417	-0.1353	-0.0467	0.1956	-0.0275	0.0669	-0.2826	0.1243	-0.0141	0.1834	0.022	-0.0281	0.1994	0.0052	0.2684	57.557	61.891	39.578
16	-0.4069	-0.418	1.0649	-0.5387	0.7248	-0.156	-0.0252	-0.0569	0.0494	-0.0087	0.0989	0.0514	-0.122	-0.0946	-0.0737	0.2076	0.0121	-0.0023	0.2187	0.0071	0.281	54.546	69.81	37.613
17	0.6931	0.2786	-0.2534	0.6375	0.4659	0.6959	0.0074	-0.0084	0.031	0.0298	0.0501	-0.0115	-0.0485	0.0391	-0.0575	0.1631	0.006	0.0086	0.1794	-0.0019	0.2619	51.343	73.469	42.39
18	3.1135	2.2188	-3.3422	2.6455	-2.6377	3.1529	0.0356	-0.0077	0.1353	0.0896	0.0582	0.0242	-0.0697	-0.1117	-0.0938	0.1709	-0.0162	0.001	0.2474	-0.0493	0.2767	68.682	86.448	45.068
19	-0.4623	-0.1	0.2176	0.4847	0.2342	-0.1462	0.0685	-0.0269	0.1004	0.115	0.0571	-0.0633	-0.0266	0.0864	-0.1257	0.1769	-0.0157	0.0173	0.2345	-0.0325	0.2814	60.181	76.026	50.385
20	1.8374	0.4358	-0.3784	2.2647	0.1968	0.6166	0.1928	-0.1713	0.2049	0.1965	0.004	-0.1309	-0.0927	0.2047	-0.1968	0.1549	0.0117	0.0084	0.228	-0.0572	0.254	68.991	73.912	50.793

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 41
2	X-RAY DIFFRACTION	2	A	42 - 57
3	X-RAY DIFFRACTION	3	A	58 - 78
4	X-RAY DIFFRACTION	4	A	79 - 113
5	X-RAY DIFFRACTION	5	A	114 - 131
6	X-RAY DIFFRACTION	6	A	132 - 151
7	X-RAY DIFFRACTION	7	A	152 - 198
8	X-RAY DIFFRACTION	8	A	199 - 221
9	X-RAY DIFFRACTION	9	A	222 - 244
10	X-RAY DIFFRACTION	10	A	245 - 263
11	X-RAY DIFFRACTION	11	B	1 - 41
12	X-RAY DIFFRACTION	12	B	42 - 57
13	X-RAY DIFFRACTION	13	B	58 - 78
14	X-RAY DIFFRACTION	14	B	79 - 113
15	X-RAY DIFFRACTION	15	B	114 - 131
16	X-RAY DIFFRACTION	16	B	132 - 151
17	X-RAY DIFFRACTION	17	B	152 - 198
18	X-RAY DIFFRACTION	18	B	199 - 221
19	X-RAY DIFFRACTION	19	B	222 - 244
20	X-RAY DIFFRACTION	20	B	245 - 263

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