PDB-4edh: The crystal structure of thymidylate kinase from Pseudomonas aeru...

ID or keywords:

Entry

Database: PDB / ID: 4edh

Title

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with ADP,TMP and Mg.

Components

Thymidylate kinase

Keywords

TRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics (MCSG) / structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Function / homology

Function and homology information

dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.32 Å

Authors

Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Citation

Journal: To be Published
Title: The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with ADP,TMP and Mg.
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.

History

Deposition	Mar 27, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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 / struct_ref_seq_dif / struct_site 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4edh.cif.gz	194 KB	Display	PDBx/mmCIF format
PDB format	pdb4edh.ent.gz	153.2 KB	Display	PDB format
PDBx/mmJSON format	4edh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4edh_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4edh_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4edh_validation.xml.gz	22.9 KB	Display
Data in CIF	4edh_validation.cif.gz	34.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ed/4edh ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4edh	HTTPS FTP

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Related structure data

Related structure data	4e5uS S: Starting model for refinement
Similar structure data	3uxm-6 2nrh-d 4gmd-1 3cd3-d 2zi4-1 5tmp-3 5mqt-1 3hjn-d 1n5k-d 3uwk-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: MCSG-APC105732

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate kinase

B: Thymidylate kinase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	45.597, 46.807, 53.101
Angle α, β, γ (deg.)	94.98, 112.33, 105.83
Int Tables number	1
Space group name H-M	P1

Details

Experimentally unknown.

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Protein , 1 types, 2 molecules AB

#1: Protein	Thymidylate kinase / dTMP kinase Mass: 23408.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

#1: Protein

Thymidylate kinase / dTMP kinase

Mass: 23408.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

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Non-polymers , 7 types, 462 molecules

#2: Chemical	ChemComp-TMP / THYMIDINE-5'-PHOSPHATE Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₈P
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.1 Å³/Da / Density % sol: 41.55 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium Sulfate, 0.1M Tris:HCl, 20% (w/v) PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirrow
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.32→25.6 Å / Num. all: 84807 / Num. obs: 84807 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.05 / Net I/σ(I): 26.3
Reflection shell	Resolution: 1.32→1.34 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.524 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4148 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E5U

4e5u

Resolution: 1.32→25.588 Å / SU ML: 0.34 / σ(F): 1.96 / Phase error: 18.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1887	4257	5.02 %	Random
R_work	0.1681	-	-	-
all	0.1692	84789	-	-
obs	0.1692	84789	94.47 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 61.159 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.7523 Å²	-3.6054 Å²	-0.2536 Å²
2-	-	0.2929 Å²	0.7886 Å²
3-	-	-	-2.0452 Å²

Refinement step

Cycle: LAST / Resolution: 1.32→25.588 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3236	0	115	453	3804

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3548
X-RAY DIFFRACTION	f_angle_d	1.206	4849
X-RAY DIFFRACTION	f_dihedral_angle_d	15.296	1397
X-RAY DIFFRACTION	f_chiral_restr	0.073	541
X-RAY DIFFRACTION	f_plane_restr	0.005	642

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 (%)
1.3199-1.3349	0.3382	114	0.3159	2501	X-RAY DIFFRACTION	86
1.3349-1.3506	0.3312	149	0.3039	2567	X-RAY DIFFRACTION	92
1.3506-1.3671	0.3003	146	0.2931	2629	X-RAY DIFFRACTION	92
1.3671-1.3844	0.3131	131	0.2697	2677	X-RAY DIFFRACTION	93
1.3844-1.4026	0.2771	124	0.256	2639	X-RAY DIFFRACTION	93
1.4026-1.4218	0.2425	155	0.2487	2652	X-RAY DIFFRACTION	93
1.4218-1.4421	0.2324	115	0.2168	2667	X-RAY DIFFRACTION	93
1.4421-1.4637	0.2303	141	0.2112	2694	X-RAY DIFFRACTION	94
1.4637-1.4865	0.2371	150	0.1939	2633	X-RAY DIFFRACTION	94
1.4865-1.5109	0.214	166	0.1904	2705	X-RAY DIFFRACTION	94
1.5109-1.537	0.1879	125	0.177	2666	X-RAY DIFFRACTION	94
1.537-1.5649	0.1957	136	0.1664	2675	X-RAY DIFFRACTION	95
1.5649-1.595	0.207	146	0.1642	2683	X-RAY DIFFRACTION	95
1.595-1.6275	0.1874	137	0.1654	2709	X-RAY DIFFRACTION	95
1.6275-1.6629	0.1623	124	0.1594	2712	X-RAY DIFFRACTION	95
1.6629-1.7016	0.2023	135	0.1631	2685	X-RAY DIFFRACTION	95
1.7016-1.7442	0.1784	154	0.1595	2732	X-RAY DIFFRACTION	95
1.7442-1.7913	0.1675	168	0.1541	2681	X-RAY DIFFRACTION	96
1.7913-1.844	0.1609	136	0.1547	2755	X-RAY DIFFRACTION	96
1.844-1.9035	0.1578	155	0.1594	2684	X-RAY DIFFRACTION	96
1.9035-1.9715	0.196	145	0.1577	2751	X-RAY DIFFRACTION	96
1.9715-2.0504	0.2068	157	0.1641	2711	X-RAY DIFFRACTION	96
2.0504-2.1437	0.1838	132	0.1585	2740	X-RAY DIFFRACTION	97
2.1437-2.2566	0.1742	129	0.1548	2759	X-RAY DIFFRACTION	96
2.2566-2.3979	0.1943	157	0.1583	2739	X-RAY DIFFRACTION	96
2.3979-2.5829	0.2	141	0.1675	2732	X-RAY DIFFRACTION	97
2.5829-2.8425	0.2043	146	0.1688	2749	X-RAY DIFFRACTION	97
2.8425-3.2531	0.1786	147	0.1672	2777	X-RAY DIFFRACTION	98
3.2531-4.0959	0.1625	160	0.1389	2726	X-RAY DIFFRACTION	96
4.0959-25.5924	0.1719	136	0.1734	2502	X-RAY DIFFRACTION	88

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	2.199	1.1621	0.5256	2.3658	-0.2584	2.2507	0.0788	-0.1557	0.0872	0.1108	-0.1189	0.0142	-0.0286	0.1259	0.02	0.1138	-0.0029	0.0082	0.117	-0.0046	0.1379	7.6655	-2.2486	8.4081
2	1.6631	-0.7557	0.9665	1.1055	-0.51	0.8079	0.0161	-0.0853	0.0335	0.0452	-0.0187	-0.0796	0.005	0.0032	0.0048	0.1517	-0.0075	0.0039	0.1299	-0.0068	0.1155	0.7124	9.176	-2.0593
3	1.2112	-0.8514	-0.0027	1.339	-0.4974	1.4865	0.1712	0.1063	-0.049	-0.2985	-0.0963	0.0728	-0.0048	0.0412	-0.0796	0.1776	0.01	-0.0222	0.0994	-0.0185	0.1098	-3.8764	-1.7399	-7.2305
4	1.1747	-0.4642	0.5387	0.3692	-0.8848	2.3981	-0.1215	-0.1457	-0.04	0.3005	0.3263	0.0648	-0.783	-0.0839	-0.2016	0.2129	0.0001	0.0654	0.2049	0.0112	0.1797	-13.9882	4.1702	9.9729
5	5.0217	-1.6468	-0.5222	3.7972	-0.5005	1.3933	-0.0098	0.15	-0.2067	-0.2208	0.12	0.3845	-0.0496	-0.2254	-0.0702	0.1483	-0.0169	-0.0503	0.1499	0.0213	0.1693	-11.7676	-7.5045	-0.3548
6	3.0901	0.3801	-3.0752	1.7133	-0.3394	7.9058	-0.2173	-0.0316	-0.4316	-0.2434	-0.1784	-0.1126	0.2919	0.3614	0.325	0.1559	0.0107	0.0186	0.1354	0.0008	0.1663	0.3382	-12.3771	3.8757
7	6.713	0.1767	-2.6382	4.7687	0.1291	6.9546	0.2345	-0.2696	-0.7032	-0.609	-0.1403	-0.5653	0.2878	0.7887	-0.0732	0.248	0.025	-0.0056	0.2616	0.0289	0.2879	10.4749	-11.4937	8.1386
8	2.6438	0.2094	-0.6945	1.4918	0.0516	1.6986	-0.1077	-0.1212	-0.2123	0.0683	-0.004	0.166	0.0961	-0.1925	0.0926	0.087	0.0086	0.014	0.1278	0.0134	0.1259	-18.6962	25.2972	-24.3728
9	7.02	0.622	1.5675	0.9434	-0.2727	1.9048	-0.0105	-0.1317	0.3035	0.158	0.0051	0.2177	-0.0417	-0.2426	0.0257	0.1463	0.0264	0.0144	0.1251	-0.0115	0.1801	-20.3167	36.1264	-23.6124
10	2.7004	-0.7318	0.8318	1.2451	-0.755	0.8772	-0.0589	0.0249	0.0426	0.1301	0.0263	0.0341	-0.1209	-0.0112	0.0681	0.1325	0.0091	0.0132	0.1076	-0.014	0.108	-10.6669	25.3503	-12.5076
11	0.8372	0.07	0.3954	0.9677	-0.4766	1.0935	0.0048	-0.004	0.01	-0.0227	-0.0013	0.0721	0.051	-0.0139	-0.0113	0.1138	0.0184	0.0095	0.1027	-0.013	0.1148	-10.3674	19.1295	-19.1133
12	4.9535	0.1853	-1.103	2.5752	-0.8229	2.2597	-0.0071	-0.0612	-0.3693	-0.2336	-0.0354	-0.0877	0.4601	0.1828	0.0226	0.2333	0.0357	0.0075	0.1476	-0.0112	0.1477	-6.7433	10.2172	-22.8707
13	1.1187	0.0412	0.0583	1.0929	-1.146	1.2505	0.1022	-0.0391	0.1177	0.196	-0.1603	-0.0474	-0.0678	0.1941	0.0848	0.1475	-0.0194	0.0155	0.1506	-0.0239	0.1325	-3.8349	29.4609	-23.4686
14	4.6991	0.725	2.0663	2.3883	0.0642	4.1228	0.0363	0.2839	-0.2141	-0.0634	-0.0057	-0.2299	0.1448	0.3925	-0.0451	0.1164	0.0357	0.0194	0.1722	0.0043	0.1333	0.5282	24.8575	-30.8147
15	2.0109	3.1949	0.4728	7.9186	0.8268	0.6881	-0.128	0.2779	0.0824	-0.097	0.2331	0.3224	0.0192	-0.0175	-0.0933	0.1432	-0.0147	-0.0038	0.1588	-0.002	0.1442	-11.1233	28.6221	-34.6924
16	5.0037	3.488	-0.057	7.3941	0.2843	2.4546	-0.2404	0.4447	0.1103	-0.7431	0.2399	0.6762	0.5001	-0.2695	-0.0069	0.2459	-0.0268	-0.0727	0.2024	0.0326	0.2135	-21.2627	33.2171	-33.6412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:30)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 31:97)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 98:138)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 139:159)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 160:176)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 177:189)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 190:209)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq -2:15)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 16:29)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 30:62)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 63:112)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 113:124)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 125:159)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 160:176)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 177:189)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 190:210)

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Protein , 1 types, 2 molecules AB

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Non-polymers , 7 types, 462 molecules

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Experimental details

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