PDB-3tek: ThermoDBP: a non-canonical single-stranded DNA binding protein wi...

ID or keywords:

Entry

Database: PDB / ID: 3tek

Title

ThermoDBP: a non-canonical single-stranded DNA binding protein with a novel structure and mechanism

Components

ThermoDBP-single stranded DNA binding protein

Keywords

DNA BINDING PROTEIN / leucine zipper / single stranded DNA binding

Function / homology

D-amino Acid Aminotransferase; Chain A, domain 1 - #50 / ssDNA-binding protein ThermoDBP / Single stranded DNA-binding protein ss DNA binding domain / D-amino Acid Aminotransferase; Chain A, domain 1 / single-stranded DNA binding / 2-Layer Sandwich / Alpha Beta / ThermoDBP-single stranded DNA binding protein

Function and homology information

Biological species

Thermoproteus tenax (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

White, M.F. / Paytubi, S. / Liu, H. / Graham, S. / McMahon, S.A. / Naismith, J.H.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.
Authors: Paytubi, S. / McMahon, S.A. / Graham, S. / Liu, H. / Botting, C.H. / Makarova, K.S. / Koonin, E.V. / Naismith, J.H. / White, M.F.

History

Deposition	Aug 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 14, 2011	Group: Database references
Revision 1.2	Feb 29, 2012	Group: Database references
Revision 1.3	Feb 28, 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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Download

PDBx/mmCIF format	3tek.cif.gz	125.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3tek.ent.gz	100.8 KB	Display	PDB format
PDBx/mmJSON format	3tek.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tek_validation.pdf.gz	426.3 KB	Display	wwPDB validaton report
Full document	3tek_full_validation.pdf.gz	428.1 KB	Display
Data in XML	3tek_validation.xml.gz	12.6 KB	Display
Data in CIF	3tek_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/te/3tek ftp://data.pdbj.org/pub/pdb/validation_reports/te/3tek	HTTPS FTP

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Related structure data

Similar structure data	4k8w-d 6s4s-3 6s4s-11 6s3y-4 2o16-1 3twu-d 6s4s-2 5s8p-2 5v7c-d 5s8q-2 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

Deposited unit

A: ThermoDBP-single stranded DNA binding protein

B: ThermoDBP-single stranded DNA binding protein

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

1

A: ThermoDBP-single stranded DNA binding protein

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

2

B: ThermoDBP-single stranded DNA binding protein

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

Unit cell

Length a, b, c (Å)	39.809, 103.655, 39.829
Angle α, β, γ (deg.)	90.00, 118.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ThermoDBP-single stranded DNA binding protein Mass: 17380.662 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoproteus tenax (archaea) / Gene: Ttx1576 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: H0USY6*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.09 Å³/Da / Density % sol: 41.07 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 11.8 % isopropanol, 0.1 M sodium citrate, 0.2 M lithium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.917 Å / Relative weight: 1
Reflection	Resolution: 2→103.65 Å / Num. obs: 19149 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2→2.051 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
SHELX	C/D/E	model building
REFMAC	5.6.0111	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SHELX	C/D/E	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→50 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.937 / SU B: 11.05 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25451	911	5.2 %	RANDOM
R_work	0.20483	-	-	-
obs	0.20738	16635	90.94 %	-
all	-	19149	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 51.163 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.04 Å²	-0 Å²	1.74 Å²
2-	-	1.32 Å²	-0 Å²
3-	-	-	2.36 Å²

Refinement step

Cycle: LAST / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2302	0	0	93	2395

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2343
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1748
X-RAY DIFFRACTION	r_angle_refined_deg	1.376	1.961	3144
X-RAY DIFFRACTION	r_angle_other_deg	1.064	3	4166
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.292	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.851	22.258	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.821	15	426
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.321	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	318
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2602
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	560
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	39	-
R_work	0.293	676	-
obs	-	-	50.46 %

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	1.8069	-3.0964	1.5166	9.7857	-3.2174	1.4559	0.0019	0.0319	0.0866	0.039	0.0585	0.0334	0.078	-0.1629	-0.0604	0.4699	-0.0475	-0.0087	0.4562	0.0314	0.3394	-9.872	-7.441	-24.916
2	3.4857	-1.1834	2.6098	3.6092	-2.5235	3.2949	0.1231	-0.0877	-0.0058	-0.3016	-0.1096	0.0491	0.2962	0.1389	-0.0135	0.5303	0.0672	-0.0128	0.395	0.0531	0.3033	1.254	-20.476	-10.122
3	2.7868	-9.9781	2.944	35.8968	-10.584	3.1212	-0.0386	0.0823	0.077	0.0522	-0.111	-0.3194	-0.0273	0.0567	0.1496	0.5169	0.0144	-0.0242	0.6496	-0.0153	0.3224	14.421	-20.506	-9.852
4	4.7745	0.2054	4.1615	0.2054	-0.4569	5.7438	0.0177	0.0378	-0.2744	-0.1011	0.0119	-0.1093	0.2922	0.044	-0.0295	0.5204	0.0182	-0.0172	0.3854	0.0078	0.3487	4.269	-16.033	-19.26
5	8.0433	3.7769	-2.448	6.2258	-0.6279	1.763	0.2037	0.3218	-0.0536	-0.096	-0.0296	-0.0772	0.3073	0.0055	-0.1741	0.5363	0.0052	-0.0357	0.4289	-0.0286	0.277	-2.074	-14.112	-32.421
6	1.6242	1.0057	0.8597	1.154	1.3219	3.0707	0.0202	0.0168	-0.1035	-0.0368	0.0212	-0.0778	-0.0534	0.249	-0.0414	0.5079	0.0037	-0.0178	0.4089	-0.0123	0.3329	7.16	-6.382	-24.136
7	1.5443	-0.1347	-2.4384	0.6771	-0.743	5.2259	-0.0023	-0.055	0.0243	0.0856	-0.0367	-0.0597	-0.0773	0.1456	0.039	0.5134	-0.0514	-0.0529	0.4395	-0.0034	0.3184	4.512	-9.833	-5.797
8	2.6288	-0.5316	1.7542	2.3352	-0.1944	1.393	0.0671	-0.0336	-0.2108	0.1575	0.0813	0.3102	-0.0338	0.2749	-0.1484	0.5305	-0.0236	0.0117	0.4457	0.0405	0.2995	-0.018	-19.143	1.621
9	0.8885	0.8927	-2.2493	1.9055	-2.1323	5.8171	0.1212	0.017	0.0773	0.0849	0.1132	0.0399	-0.0861	0.0345	-0.2343	0.4984	-0.0078	-0.0236	0.4032	-0.0026	0.3706	-3.049	-5.949	-18.892
10	1.4145	-3.9548	1.9111	11.0823	-5.3461	2.5903	-0.1344	-0.122	-0.0926	0.3767	0.3023	0.3429	-0.192	-0.2103	-0.1679	0.5271	0.0291	0.0542	0.3745	0.0768	0.4051	-5.369	-20.832	0.113
11	13.6371	12.5313	16.9841	11.5902	15.6153	21.1807	-0.7317	-0.121	-0.933	-1.5662	0.9253	-0.9999	-2.0833	-0.1632	-0.1936	0.5889	-0.118	-0.0785	0.4375	-0.4614	0.8697	-12.09	15.707	-14.028
12	1.5863	0.4481	-0.0445	2.7407	2.0587	1.6711	0.0116	0.1287	0.0151	0.004	-0.021	-0.0798	0.0071	-0.1378	0.0094	0.5046	-0.0241	-0.0211	0.4559	-0.0002	0.3276	-16.907	0.037	-19.518
13	4.0116	2.2754	-0.5863	1.9821	0.4299	0.9647	-0.087	-0.2107	0.5314	0.0543	-0.0506	0.3855	0.1385	0.1085	0.1376	0.4758	-0.0331	-0.0243	0.3656	-0.0974	0.4561	-8.818	15.116	-0.449
14	9.1366	14.0149	1.7967	30.7365	7.2923	2.5862	0.0822	-1.4585	1.4752	1.1415	-0.0792	1.5352	0.6009	0.7184	-0.0029	0.5858	0.1027	-0.0693	0.9046	-0.2819	0.3981	-15.505	13.557	8.081
15	3.6273	0.0916	4.3066	0.3925	-1.2549	9.9678	-0.054	-0.139	0.114	0.0517	0.0448	0.0594	-0.4392	-0.2142	0.0092	0.5389	0.0027	-0.0034	0.3963	-0.017	0.343	-18.612	9.321	-4.573
16	3.8601	1.281	-0.9765	0.956	-1.3139	2.1995	-0.0511	0.1374	0.3302	0.0701	0.0381	0.0549	-0.1174	-0.2327	0.013	0.5057	0.0179	-0.0153	0.4135	0.0051	0.3621	-27.557	6.656	-15.591
17	2.5816	-4.005	1.4572	6.3807	-1.8683	7.1787	-0.1147	-0.1863	-0.0277	0.239	0.1745	0.1596	-0.1093	-0.1742	-0.0598	0.4821	-0.0257	-0.0008	0.4081	-0.0201	0.342	-25.695	-1.516	-5.594
18	6.0359	2.9859	-0.2703	1.9206	0.1794	0.2339	0.1401	-0.0863	-0.0707	0.1248	-0.0678	-0.1268	0.0337	-0.0269	-0.0722	0.4983	-0.0331	-0.0444	0.4439	0.0242	0.3124	-6.264	3.233	0.322
19	1.6672	0.9883	0.9841	0.6932	0.5829	1.3869	-0.019	-0.1325	-0.1034	-0.1623	0.0661	-0.1322	-0.2225	-0.0843	-0.047	0.5045	-0.0288	-0.0194	0.4057	-0.0321	0.3541	-6.048	9.886	-3.781
20	0.71	0.1993	0.5066	0.8124	0.6989	0.7739	0.015	-0.1197	-0.0366	-0.1024	0.0951	-0.0935	-0.0522	-0.0098	-0.11	0.5192	-0.0165	-0.0035	0.3762	0.0135	0.3748	-7.098	4.122	-8.815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 28
2	X-RAY DIFFRACTION	2	A	29 - 41
3	X-RAY DIFFRACTION	3	A	42 - 50
4	X-RAY DIFFRACTION	4	A	51 - 64
5	X-RAY DIFFRACTION	5	A	65 - 75
6	X-RAY DIFFRACTION	6	A	76 - 89
7	X-RAY DIFFRACTION	7	A	90 - 102
8	X-RAY DIFFRACTION	8	A	103 - 119
9	X-RAY DIFFRACTION	9	A	120 - 134
10	X-RAY DIFFRACTION	10	A	135 - 148
11	X-RAY DIFFRACTION	11	B	10 - 15
12	X-RAY DIFFRACTION	12	B	16 - 30
13	X-RAY DIFFRACTION	13	B	31 - 41
14	X-RAY DIFFRACTION	14	B	42 - 50
15	X-RAY DIFFRACTION	15	B	51 - 63
16	X-RAY DIFFRACTION	16	B	64 - 77
17	X-RAY DIFFRACTION	17	B	78 - 85
18	X-RAY DIFFRACTION	18	B	86 - 108
19	X-RAY DIFFRACTION	19	B	109 - 126
20	X-RAY DIFFRACTION	20	B	127 - 143

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