PDB-4wop: Nucleotide Triphosphate Promiscuity in Mycobacterium tuberculosis...

ID or keywords:

Entry

Database: PDB / ID: 4wop

Title

Nucleotide Triphosphate Promiscuity in Mycobacterium tuberculosis Dethiobiotin Synthetase

Components

ATP-dependent dethiobiotin synthetase BioD

Keywords

LIGASE /

biotin protein ligase

Function / homology

Function and homology information

dethiobiotin synthase /

dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding /

ATP binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.393 Å

Authors

Salaemae, W. / Yap, M.Y. / Wegener, K.L. / Booker, G.W. / Wilce, M.C.J. / Polyak, S.W.

Citation

Journal: Tuberculosis (Edinb) / Year: 2015
Title: Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase.
Authors: Salaemae, W. / Yap, M.Y. / Wegener, K.L. / Booker, G.W. / Wilce, M.C. / Polyak, S.W.

History

Deposition	Oct 16, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2015	Group: Database references
Revision 1.2	May 27, 2015	Group: Structure summary
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wop.cif.gz	332 KB	Display	PDBx/mmCIF format
PDB format	pdb4wop.ent.gz	272.3 KB	Display	PDB format
PDBx/mmJSON format	4wop.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/wo/4wop ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wop	HTTPS FTP

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Related structure data

Similar structure data	6nvd-1 6cve-1 6nmz-1 6nnz-1 6e06-1 6cze-2 6cvf-1 6nve-2 6nmz-2 6nwg-1 6cze-1 6cvv-2 6cvf-2 6cvv-1 6nkb-1 6nvc-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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: ATP-dependent dethiobiotin synthetase BioD

B: ATP-dependent dethiobiotin synthetase BioD

C: ATP-dependent dethiobiotin synthetase BioD

D: ATP-dependent dethiobiotin synthetase BioD

hetero molecules

91.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-dependent dethiobiotin synthetase BioD

B: ATP-dependent dethiobiotin synthetase BioD

hetero molecules

defined by author&software
45.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ATP-dependent dethiobiotin synthetase BioD

D: ATP-dependent dethiobiotin synthetase BioD

hetero molecules

defined by author&software
45.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.560, 104.330, 152.340
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ATP-dependent dethiobiotin synthetase BioD / DTB synthetase / DTBS / Dethiobiotin synthase Mass: 22356.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: bioD, MRA_1582 / Production host: Escherichia coli (E. coli) References: UniProt: A5U2S7, UniProt: P9WPQ5*PLUS, dethiobiotin synthase
#2: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.43 Å³/Da / Density % sol: 49.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystals grew from the following range of buffers: 0.8 - 1.2 M ammonium sulphate, 0.1 M Tris pH 7 - 8.5 with 10 % glycerol.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 9, 2013

Radiation

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

Radiation wavelength

Wavelength: 1.54178 Å / Relative weight: 1

Reflection

Resolution: 2.39→37 Å / Num. all: 182745 / Num. obs: 64617 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / R_merge F obs: 0.992 / R_merge(I) obs: 0.105 / R_rim(I) all: 0.13 / Χ²: 0.983 / Net I/σ(I): 9.3 / Num. measured all: 182745

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.39-2.54		0.695	0.554	1.94	27990	10681	10151	0.692	95
2.54-2.71		0.801	0.406	2.63	28555	10079	10056	0.505	99.8
2.71-2.93		0.892	0.268	4.11	26573	9315	9302	0.332	99.9
2.93-3.21		0.954	0.167	6.46	24853	8679	8664	0.207	99.8
3.21-3.58		0.986	0.098	10.68	21997	7757	7668	0.122	98.9
3.58-4.13		0.99	0.068	16.21	16139	6895	6080	0.086	88.2
4.13-5.05		0.996	0.046	20.63	16514	5811	5716	0.057	98.4
5.05-7.1		0.995	0.05	18.67	12979	4489	4471	0.062	99.6
	7.1	0.999	0.025	31.36	7145	2546	2509	0.03	98.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Resolution: 2.393→37 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 27.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2531	3247	5.03 %
R_work	0.1805	61358	-
obs	0.1842	64605	97.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 110.42 Å² / B_iso mean: 38.0978 Å² / B_iso min: 15.72 Å²

Refinement step

Cycle: final / Resolution: 2.393→37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6257	0	112	344	6713
B_iso mean	-	-	55.79	36.48	-
Num. residues	-	-	-	-	900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6476
X-RAY DIFFRACTION	f_angle_d	1.094	8884
X-RAY DIFFRACTION	f_chiral_restr	0.039	1115
X-RAY DIFFRACTION	f_plane_restr	0.006	1151
X-RAY DIFFRACTION	f_dihedral_angle_d	14.824	2249

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3932-2.4289	0.3655	120	0.3144	2243	2363	82
2.4289-2.4669	0.379	146	0.2762	2752	2898	100
2.4669-2.5073	0.2928	148	0.2449	2717	2865	100
2.5073-2.5505	0.3805	143	0.2472	2697	2840	100
2.5505-2.5969	0.3074	149	0.2472	2801	2950	100
2.5969-2.6468	0.3303	140	0.249	2661	2801	100
2.6468-2.7009	0.3577	144	0.2334	2749	2893	100
2.7009-2.7596	0.2956	146	0.2097	2724	2870	100
2.7596-2.8238	0.2778	145	0.208	2716	2861	100
2.8238-2.8944	0.264	147	0.2082	2752	2899	100
2.8944-2.9726	0.244	146	0.1852	2712	2858	100
2.9726-3.0601	0.2667	145	0.1902	2741	2886	100
3.0601-3.1588	0.276	141	0.1923	2728	2869	100
3.1588-3.2717	0.2837	140	0.175	2742	2882	100
3.2717-3.4026	0.2348	145	0.1711	2736	2881	100
3.4026-3.5575	0.2571	143	0.1779	2677	2820	99
3.5575-3.7449	0.2836	136	0.1994	2530	2666	93
3.7449-3.9794	0.2598	132	0.1716	2580	2712	94
3.9794-4.2865	0.2676	116	0.195	2242	2358	82
4.2865-4.7175	0.1755	140	0.1257	2718	2858	99
4.7175-5.3992	0.2145	141	0.1314	2734	2875	99
5.3992-6.7989	0.2119	145	0.139	2719	2864	100
6.7989-46.0913	0.1417	149	0.1167	2687	2836	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	2.837	0.311	-0.2038	2.4773	-0.0032	3.0247	-0.0043	-0.3129	0.3269	-0.1901	0.1473	-0.0812	-0.1542	-0.1493	0.0598	0.2929	0.0419	0.0355	0.2159	-0.0228	0.1892	14.3714	28.6649	-14.6123
2	4.3507	1.7751	-0.4393	2.1329	0.3364	1.4812	-0.0636	-0.1815	0.0909	-0.044	-0.0641	0.0525	-0.2271	0.0714	-0.0303	0.4051	-0.0125	0.0225	0.3077	-0.0362	0.2408	22.4417	35.7273	-12.183
3	2.8259	0.4922	-0.2138	1.7393	0.2161	2.1052	0.1021	-0.1128	0.4642	0.4246	-0.107	0.1675	-0.3079	0.0186	0.0106	0.49	-0.0302	-0.0063	0.3022	-0.0548	0.2969	22.9187	37.8783	-12.3079
4	3.1623	0.8239	0.6248	5.0347	-0.5415	2.5346	0.268	-0.1894	0.1252	0.2436	-0.25	-0.4861	-0.055	0.6284	0.0544	0.4509	-0.1187	-0.0357	0.4987	-0.0096	0.2293	38.9395	34.1663	-15.0249
5	3.3199	0.3298	-0.0091	1.6798	0.2698	1.8415	-0.0497	-0.8279	0.1335	0.3276	-0.0221	0.0116	0.2047	0.1371	0.0499	0.4387	0	-0.0047	0.4638	0.0184	0.2194	22.7083	25.9107	-3.5376
6	2.2166	0.7373	-0.0914	5.4156	0.483	5.8638	0.0647	0.0652	0.0458	0.3066	-0.1767	-0.3799	-0.2973	0.7453	0.0546	0.4118	-0.0287	-0.0121	0.3214	0.0162	0.1919	32.4377	24.1819	-16.5728
7	2.3228	0.6344	-0.2372	2.3111	0.0643	3.4909	-0.1394	-0.0829	-0.242	-0.1581	0.041	-0.124	0.0258	-0.0371	0.0607	0.3268	-0.01	0.0192	0.2506	0.0112	0.2594	21.7925	18.8302	-21.5072
8	2.9826	0.7927	0.262	2.3409	0.4226	4.1267	0.0303	-0.1541	0.172	-0.2008	0.022	0.2452	-0.3302	-0.3453	0.0313	0.2576	0.0211	0.0307	0.2167	0.0036	0.1903	11.6718	24.2055	-25.142
9	2.474	0.5756	-0.0082	3.2126	-1.7137	5.6312	-0.3513	0.1756	0.0155	-0.3718	-0.0701	0.0741	0.5519	-0.1896	0.1089	0.4334	-0.0112	-0.0879	0.3511	-0.0486	0.3392	9.3906	19.773	-32.9569
10	2.2939	0.2689	-0.2603	2.7103	0.2772	3.029	0.0917	0.0631	0.171	0.1941	-0.1954	0.4734	-0.4185	-0.6491	0.0726	0.2152	0.0306	-0.0166	0.3766	-0.0651	0.2667	5.5056	29.2326	-17.2257
11	2.9299	1.1604	0.0978	1.5936	1.3378	2.2536	0.0256	0.1351	-0.011	0.0335	-0.0715	0.1807	0.1811	-0.2005	0.0833	0.3678	0.0063	0.0038	0.2551	0.007	0.2433	27.7466	14.6516	-49.1328
12	1.8639	0.5987	-0.3826	2.1378	0.3179	3.0787	0.0084	-0.0722	-0.0628	0.2186	0.0255	-0.0764	0.0186	0.1686	-0.039	0.274	0.0159	-0.0157	0.2424	-0.0223	0.2145	35.7355	20.3936	-37.5463
13	2.5651	1.1765	-0.4458	1.3857	1.005	3.0119	0.005	-0.1042	0.3782	-0.1033	-0.0004	-0.0708	-0.5941	-0.279	0.0884	0.4104	0.0331	-0.0124	0.211	-0.033	0.3955	-2.1143	1.7555	-23.4057
14	2.4834	0.4612	-0.2221	2.5988	0.3572	2.1205	-0.0356	0.1376	-0.0826	-0.1885	0.1018	0.201	-0.1142	-0.0366	-0.1007	0.3617	0.0354	-0.0355	0.2266	-0.0157	0.2227	4.87	-7.8806	-29.1601
15	3.5985	0.3037	0.9165	2.6135	0.3552	3.6752	0.0279	0.5006	0.3089	-0.0886	0.1918	0.1925	-0.1207	0.1951	-0.0568	0.3316	0.0319	0.0068	0.2133	0.0166	0.2915	5.3324	3.6187	-27.4689
16	2.1379	0.294	0.2842	2.3861	0.7638	3.2102	0.0229	-0.2397	0.0191	-0.0849	-0.1248	0.5762	0.0497	-0.455	-0.0175	0.2277	0.0673	0.0061	0.3016	0.0186	0.3936	-7.0405	-5.9343	-15.797
17	1.6196	0.4633	0.0712	1.3695	-0.3946	4.2368	0.0028	0.0438	-0.2623	0.0496	-0.0464	-0.0984	0.2029	0.2744	-0.0361	0.3875	0.0395	-0.0085	0.3067	0.0228	0.3052	12.5661	-11.4047	12.1242
18	3.2223	1.0188	0.4871	2.12	-0.1596	4.1114	0.066	0.0736	0.2168	0.1076	-0.1034	0.2367	-0.0504	-0.2479	-0.0756	0.3341	0.0109	0.023	0.2566	0.0133	0.193	0.8147	-6.7882	14.0315
19	2.6705	0.1728	0.0192	5.087	-0.4458	7.626	-0.0511	0.0089	0.1011	0.0457	-0.0062	0.7623	0.0457	-0.6691	-0.0747	0.3579	-0.0046	0.0757	0.3509	0.0472	0.2468	-1.3795	-2.9729	5.3342
20	1.0545	0.4536	0.015	1.8027	-0.2071	4.6849	0.0642	0.1428	-0.0934	-0.2958	0.0014	-0.1177	0.0161	0.5511	-0.0311	0.3483	0.0358	0.0174	0.306	0.0127	0.2541	14.3501	-3.3919	-3.4993
21	2.1344	0.3012	0.0723	3.1263	-0.1073	5.1367	0.3362	0.2179	-0.3439	0.6306	-0.4178	-0.4339	0.2784	1.2476	0.0167	0.323	0.0717	-0.0255	0.5973	0.0044	0.3226	24.6003	-10.2511	6.9923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 29 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 48 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 73 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 74 through 87 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 88 through 108 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 109 through 123 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 124 through 159 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 176 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 177 through 189 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 190 through 225 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 108 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 109 through 225 )	B
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -2 through 14 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 15 through 87 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 88 through 123 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 124 through 225 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 63 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 64 through 108 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 109 through 123 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 124 through 189 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 190 through 225 )	D

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