PDB-4e5u: The crystal structure of thymidylate kinase from Pseudomonas aeru...

ID or keywords:

Entry

Database: PDB / ID: 4e5u

Title

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with thymidine monophosphate.

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 / phosphorylation / ATP binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.812 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 thymidine monophosphate.
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.

History

Deposition	Mar 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 28, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4e5u.cif.gz	176.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4e5u.ent.gz	149 KB	Display	PDB format
PDBx/mmJSON format	4e5u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4e5u_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4e5u_full_validation.pdf.gz	1 MB	Display
Data in XML	4e5u_validation.xml.gz	19.3 KB	Display
Data in CIF	4e5u_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e5/4e5u ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5u	HTTPS FTP

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Related structure data

Similar structure data	1n5l-d 4s35-d 4qga-d 5iz8-2 5tmp-3 4gfd-d 5zax-d 5x8k-d 4s2e-d 5xak-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: MCSG-APC105732

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate kinase

B: Thymidylate kinase

hetero molecules

47.9 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)	46.132, 57.399, 149.952
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Experimentally unknown

#1: Protein	Thymidylate kinase / dTMP kinase Mass: 23549.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (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
#2: Chemical	ChemComp-TMP / THYMIDINE-5'-PHOSPHATE Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₈P
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.11 Å³/Da / Density % sol: 41.64 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Calsium Chloride, 0.1M Tris:HCl, 32% (w/v) PEG4000, 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: 0.97915 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2011 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.812→36 Å / Num. all: 36891 / Num. obs: 36891 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / R_merge(I) obs: 0.084 / Net I/σ(I): 37.9
Reflection shell	Resolution: 1.82→1.85 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.636 / Mean I/σ(I) obs: 3 / Num. unique all: 1837 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
RESOLVE		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.812→35.958 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 22.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2309	1838	4.99 %	random
R_work	0.1884	-	-	-
all	0.1905	36812	-	-
obs	0.1905	36812	99.21 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.1 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.5261 Å²	-0 Å²	0 Å²
2-	-	-6.9425 Å²	-0 Å²
3-	-	-	5.4164 Å²

Refinement step

Cycle: LAST / Resolution: 1.812→35.958 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3195	0	45	220	3460

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3295
X-RAY DIFFRACTION	f_angle_d	0.998	4468
X-RAY DIFFRACTION	f_dihedral_angle_d	14.251	1256
X-RAY DIFFRACTION	f_chiral_restr	0.064	502
X-RAY DIFFRACTION	f_plane_restr	0.005	599

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 (%)
1.8117-1.8607	0.2991	118	0.2431	2464	X-RAY DIFFRACTION	92
1.8607-1.9155	0.2525	144	0.2281	2674	X-RAY DIFFRACTION	100
1.9155-1.9773	0.2797	150	0.2045	2645	X-RAY DIFFRACTION	100
1.9773-2.048	0.2494	152	0.204	2659	X-RAY DIFFRACTION	100
2.048-2.13	0.2416	140	0.1933	2673	X-RAY DIFFRACTION	100
2.13-2.2269	0.2335	147	0.1972	2675	X-RAY DIFFRACTION	100
2.2269-2.3443	0.2752	123	0.1892	2692	X-RAY DIFFRACTION	100
2.3443-2.4911	0.2338	141	0.1947	2703	X-RAY DIFFRACTION	100
2.4911-2.6834	0.2756	134	0.1975	2711	X-RAY DIFFRACTION	100
2.6834-2.9533	0.2567	157	0.2065	2698	X-RAY DIFFRACTION	100
2.9533-3.3804	0.2307	143	0.2002	2745	X-RAY DIFFRACTION	100
3.3804-4.2578	0.2036	138	0.168	2770	X-RAY DIFFRACTION	100
4.2578-35.965	0.202	151	0.1724	2865	X-RAY DIFFRACTION	98

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	3.3262	-2.7053	-2.4432	7.4922	5.4448	4.1919	0.0989	-0.1038	0.0063	0.4796	0.0736	-0.1647	-0.0495	-0.0858	-0.068	0.2969	0.0522	0.026	0.2047	0.0293	0.1734	22.7651	-30.852	62.6383
2	8.5048	-3.3457	-1.9106	7.2051	-1.2015	5.8128	0.1018	-0.8418	-0.2802	0.7836	0.2211	-0.9195	0.563	0.8727	0.0439	0.2694	0.0885	-0.0857	0.3525	0.0155	0.4437	34.3551	-37.2963	64.5388
3	2.4059	-2.6617	-0.051	6.4544	0.1487	0.8512	-0.316	-0.2708	-0.0649	0.2736	0.0803	-0.4566	0.1485	0.3183	0.051	0.1472	0.0487	0.0081	0.2789	0.0409	0.277	29.9772	-26.4377	58.5319
4	3.0898	-1.7161	-0.9929	4.2623	0.8974	2.9413	-0.1383	-0.6546	0.5282	0.5683	0.2641	-0.4163	-0.2901	0.2425	-0.1443	0.267	0.0448	-0.0524	0.2866	-0.0629	0.2262	20.9709	-9.4162	65.1732
5	1.907	-0.5978	0.361	4.1106	-0.0755	1.7373	-0.0799	-0.0884	0.0057	0.2635	0.0437	0.0287	0.1458	-0.0095	0.022	0.1714	0.0333	0.0073	0.1725	0.0127	0.1533	18.5185	-22.2113	58.7303
6	1.9408	-0.4241	-0.0445	3.2943	-0.2973	2.2798	0.0623	-0.1852	-0.1069	0.1565	-0.0043	0.5556	0.2451	-0.0748	-0.0372	0.2392	0.0179	0.0449	0.2133	0.0079	0.2224	13.4475	-27.238	58.6695
7	3.1128	0.7052	1.4467	4.9375	-1.8608	3.7722	0.0968	-1.0732	-0.2081	1.2857	-0.1732	-0.4164	0.0931	0.2254	0.0334	0.7723	0.1005	-0.1123	0.5605	-0.0058	0.2518	19.7673	-18.5129	78.3553
8	3.3653	1.8771	1.7117	3.6311	-0.1317	4.4804	-0.1231	-0.9444	-0.1651	1.11	-0.351	0.5366	-0.0907	-0.5812	-0.1118	0.5384	0.037	0.3234	0.3319	0.1724	0.2489	9.3836	-28.194	71.9423
9	3.1892	0.6515	4.7084	3.8906	0.4185	8.6842	0.2797	-0.7206	-0.3507	1.1324	-0.0356	-0.0095	0.3673	0.4115	-0.2125	0.4238	0.0295	0.0753	0.3293	0.0691	0.2754	17.6324	-38.3899	68.708
10	6.1679	-1.8329	0.5435	3.2019	-0.5087	8.4137	0.1013	-0.3335	-1.0818	0.604	-0.2403	-0.2596	0.8622	0.4328	-0.0317	0.4801	-0.0012	-0.1085	0.2556	0.1006	0.4377	26.8498	-43.4176	64.6597
11	9.8201	-4.7332	-5.6712	6.7352	3.1435	3.4676	0.2724	-0.5847	0.4572	-0.0834	0.0201	-0.3817	-0.5181	0.5276	-0.2889	0.2358	0.03	-0.0102	0.307	0.0108	0.1317	7.9312	7.0961	47.8899
12	6.6449	-4.4297	-2.0831	5.1646	3.4124	6.751	0.2454	0.2653	0.9412	-0.3126	0.3314	-1.0674	-0.933	0.3316	-0.4058	0.3286	0.0178	0.0989	0.2448	-0.1005	0.8126	5.0485	19.1164	52.4967
13	1.8527	-0.6964	0.6702	2.6458	-0.5249	1.9406	-0.1754	-0.0353	0.093	-0.0514	0.1732	0.055	-0.2065	-0.0601	-0.0066	0.0486	0.0377	-0.0017	0.0517	0.0155	0.0715	11.3437	-1.7161	51.3652
14	6.1029	0.9276	-1.2124	2.0617	-0.0599	2.6387	-0.0598	-0.1286	0.7129	-0.0692	-0.4157	-0.7951	-1.239	0.8298	0.2618	0.5336	-0.106	-0.0178	0.3264	0.023	0.3925	26.2261	5.7564	42.6813
15	2.3755	-2.2148	-2.0663	5.4886	-1.7343	5.7056	0.0753	0.4577	-0.0926	-0.5804	-0.0657	-0.0645	-0.0619	-0.2493	0.0104	0.3342	-0.0324	-0.0213	0.2404	-0.0131	0.1711	13.6517	0.5785	34.7923
16	1.7608	-1.5154	-2.2481	2.0672	1.4092	3.9483	0.7918	0.5869	0.8787	-0.6582	0.0061	0.0288	-1.356	-0.6022	-0.5807	0.5976	0.1907	0.1652	0.4275	0.1392	0.5475	1.5125	14.4118	41.8713

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:17)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 18:30)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 31:43)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 44:62)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 63:112)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 113:138)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 139:159)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 160:176)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 177:189)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 190:210)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 2:17)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 18:30)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 31:138)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 139:159)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 160:176)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 177:209)

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