PDB-4uxj: Leishmania major Thymidine Kinase in complex with dTTP

ID or keywords:

Entry

Database: PDB / ID: 4uxj

Title

Leishmania major Thymidine Kinase in complex with dTTP

Components

THYMIDINE KINASE

Keywords

TRANSFERASE

Function / homology

Function and homology information

thymidine metabolic process /

thymidine kinase /

thymidine kinase activity / DNA biosynthetic process /

phosphorylation /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

LEISHMANIA MAJOR (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Timm, J. / Bosch-Navarrete, C. / Recio, E. / Nettleship, J.E. / Rada, H. / Gonzalez-Pacanowska, D. / Wilson, K.S.

Citation

Journal: Plos Negl Trop Dis / Year: 2015
Title: Structural and Kinetic Characterization of Thymidine Kinase from Leishmania Major.
Authors: Timm, J. / Bosch-Navarrete, C. / Recio, E. / Nettleship, J.E. / Rada, H. / Gonzalez-Pacanowska, D. / Wilson, K.S.

History

Deposition	Aug 22, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 27, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4uxj.cif.gz	508.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4uxj.ent.gz	428.4 KB	Display	PDB format
PDBx/mmJSON format	4uxj.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/ux/4uxj ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4uxj	HTTPS FTP

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Related structure data

Related structure data	4uxhC 4uxiC C: citing same article (ref.)
Similar structure data	2j87-d 4uxh-1 5fuy-2 5fuv-1 1o90-d 6faj-d 2orv-1 5fuw-1 3rv2-d 6fwb-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4uxhC

4uxiC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: THYMIDINE KINASE

B: THYMIDINE KINASE

C: THYMIDINE KINASE

D: THYMIDINE KINASE

E: THYMIDINE KINASE

F: THYMIDINE KINASE

G: THYMIDINE KINASE

H: THYMIDINE KINASE

hetero molecules

180 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: THYMIDINE KINASE

F: THYMIDINE KINASE

hetero molecules

G: THYMIDINE KINASE

H: THYMIDINE KINASE

hetero molecules

defined by author&software
90.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: THYMIDINE KINASE

H: THYMIDINE KINASE

hetero molecules

E: THYMIDINE KINASE

F: THYMIDINE KINASE

hetero molecules

defined by author&software
90.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: THYMIDINE KINASE

B: THYMIDINE KINASE

C: THYMIDINE KINASE

D: THYMIDINE KINASE

hetero molecules

defined by author&software
90.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.600, 61.630, 110.090
Angle α, β, γ (deg.)	81.07, 85.80, 74.94
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	3 - 178
2	1	B	3 - 178
1	2	A	3 - 179
2	2	C	3 - 179
1	3	A	3 - 179
2	3	D	3 - 179
1	4	A	3 - 179
2	4	E	3 - 179
1	5	A	3 - 181
2	5	F	3 - 181
1	6	A	3 - 179
2	6	G	3 - 179
1	7	A	3 - 177
2	7	H	3 - 177
1	8	B	3 - 179
2	8	C	3 - 179
1	9	B	3 - 179
2	9	D	3 - 179
1	10	B	3 - 179
2	10	E	3 - 179
1	11	B	3 - 179
2	11	F	3 - 179
1	12	B	3 - 179
2	12	G	3 - 179
1	13	B	3 - 177
2	13	H	3 - 177
1	14	C	3 - 179
2	14	D	3 - 179
1	15	C	3 - 179
2	15	E	3 - 179
1	16	C	3 - 178
2	16	F	3 - 178
1	17	C	3 - 179
2	17	G	3 - 179
1	18	C	3 - 177
2	18	H	3 - 177
1	19	D	3 - 179
2	19	E	3 - 179
1	20	D	3 - 179
2	20	F	3 - 179
1	21	D	3 - 179
2	21	G	3 - 179
1	22	D	3 - 176
2	22	H	3 - 176
1	23	E	3 - 178
2	23	F	3 - 178
1	24	E	3 - 179
2	24	G	3 - 179
1	25	E	3 - 177
2	25	H	3 - 177
1	26	F	3 - 179
2	26	G	3 - 179
1	27	F	3 - 177
2	27	H	3 - 177
1	28	G	3 - 177
2	28	H	3 - 177

NCS ensembles :

#1: Protein	THYMIDINE KINASE / Mass: 21978.266 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q4QC75, thymidine kinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.26 Å³/Da / Density % sol: 45.7 % / Description: NONE
Crystal grow	pH: 8 Details: 50 MM HEPES PH 8.0, 36% (W/V) PENTA-ERYTHRITOL-PROPOXYLATE, 1 MM DTTP, 3 MM MGCL2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Feb 1, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 3→59.54 Å / Num. obs: 29290 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / R_merge(I) obs: 0.14 / Net I/σ(I): 6.2
Reflection shell	Resolution: 3→3.16 Å / Redundancy: 2 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→108.69 Å / Cor.coef. F_o:F_c: 0.869 / Cor.coef. F_o:F_c free: 0.845 / SU B: 49.337 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27837	1404	4.8 %	RANDOM
R_work	0.2603	-	-	-
obs	0.26118	27884	94.7 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.128 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	1.01 Å²	-2.72 Å²
2-	-	-0.39 Å²	-0.69 Å²
3-	-	-	0.82 Å²

Refinement step

Cycle: LAST / Resolution: 3→108.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9673	0	232	53	9958

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	10083
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	9057
X-RAY DIFFRACTION	r_angle_refined_deg	1.445	1.98	13703
X-RAY DIFFRACTION	r_angle_other_deg	1.218	3.003	20554
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.904	5	1316
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.447	23.281	381
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.625	15	1457
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.882	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1590
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11433
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2245
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	1.424	2.155	5312
X-RAY DIFFRACTION	r_mcbond_other	1.424	2.155	5311
X-RAY DIFFRACTION	r_mcangle_it	2.417	3.228	6612
X-RAY DIFFRACTION	r_mcangle_other	2.416	3.229	6613
X-RAY DIFFRACTION	r_scbond_it	1.94	2.262	4771
X-RAY DIFFRACTION	r_scbond_other	1.917	2.253	4747
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.757	3.358	7052
X-RAY DIFFRACTION	r_long_range_B_refined	4.957	17.489	10911
X-RAY DIFFRACTION	r_long_range_B_other	4.94	17.46	10888
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7935	0.09
1	2	B	7935	0.09
2	1	A	8186	0.1
2	2	C	8186	0.1
3	1	A	7576	0.08
3	2	D	7576	0.08
4	1	A	8270	0.09
4	2	E	8270	0.09
5	1	A	8160	0.08
5	2	F	8160	0.08
6	1	A	8073	0.09
6	2	G	8073	0.09
7	1	A	7221	0.09
7	2	H	7221	0.09
8	1	B	8583	0.09
8	2	C	8583	0.09
9	1	B	7529	0.07
9	2	D	7529	0.07
10	1	B	8105	0.1
10	2	E	8105	0.1
11	1	B	8379	0.08
11	2	F	8379	0.08
12	1	B	8079	0.09
12	2	G	8079	0.09
13	1	B	7389	0.08
13	2	H	7389	0.08
14	1	C	7581	0.09
14	2	D	7581	0.09
15	1	C	8504	0.11
15	2	E	8504	0.11
16	1	C	8373	0.08
16	2	F	8373	0.08
17	1	C	8832	0.08
17	2	G	8832	0.08
18	1	C	7544	0.09
18	2	H	7544	0.09
19	1	D	7689	0.08
19	2	E	7689	0.08
20	1	D	7462	0.08
20	2	F	7462	0.08
21	1	D	7455	0.08
21	2	G	7455	0.08
22	1	D	6929	0.08
22	2	H	6929	0.08
23	1	E	7945	0.1
23	2	F	7945	0.1
24	1	E	8282	0.1
24	2	G	8282	0.1
25	1	E	7208	0.1
25	2	H	7208	0.1
26	1	F	8011	0.1
26	2	G	8011	0.1
27	1	F	7437	0.07
27	2	H	7437	0.07
28	1	G	7208	0.09
28	2	H	7208	0.09

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	119	-
R_work	0.369	2090	-
obs	-	-	94.81 %

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	3.2702	-0.6804	0.477	0.4702	0.904	3.3566	-0.5224	-0.005	0.213	-0.211	0.1105	0.0978	-0.9661	0.2089	0.4119	0.4573	-0.1422	-0.2018	0.1063	0.0658	0.1197	-0.0872	7.5583	25.0588
2	2.2516	0.0084	1.2855	1.0829	0.5661	2.8008	-0.2641	-0.2835	0.279	0.1118	-0.1231	-0.0401	-0.2337	-0.2416	0.3872	0.3104	0.135	-0.0636	0.2867	-0.109	0.0999	0.0252	2.3532	49.3456
3	2.7646	0.5115	1.8349	1.6313	0.672	3.2806	0.0543	0.1451	-0.1326	0.2087	0.1531	-0.0475	0.3949	0.245	-0.2075	0.1394	-0.0155	0.0299	0.1306	-0.0567	0.0597	-4.1097	-18.2015	19.2738
4	3.7313	-0.6976	1.7335	1.3279	1.4272	3.9195	0.3315	-0.5603	-0.2683	0.5838	-0.184	0.0576	0.8401	-0.6683	-0.1476	0.5217	-0.1702	0.0232	0.2312	0.0843	0.0503	-10.0069	-20.9165	42.8639
5	1.5863	0.0552	1.0521	0.0279	0.0613	2.3176	0.0831	0.3403	-0.0468	-0.0475	-0.0409	0.0604	0.1207	0.1532	-0.0422	0.3997	0.1567	-0.0941	0.2835	-0.1226	0.1565	21.5785	-17.9375	72.4682
6	0.437	-0.4065	0.8721	2.5805	0.3751	2.411	0.148	-0.2226	-0.0045	-0.1753	-0.2295	0.1742	0.207	-0.6463	0.0815	0.192	-0.0779	-0.0046	0.3716	-0.0548	0.0916	17.0593	-15.8638	97.3969
7	2.5101	0.8192	0.8991	0.7369	1.2158	2.3118	0.3525	0.2	-0.2392	0.2267	0.0219	-0.1925	0.4205	0.2237	-0.3744	0.27	0.089	-0.1213	0.2858	-0.0503	0.1459	-18.422	-19.6099	102.6216
8	0.743	0.5488	1.0657	3.2783	0.2772	2.2834	0.1242	0.7169	-0.108	-0.0909	0.1322	-0.291	0.0393	1.0263	-0.2564	0.1337	0.1783	0.041	0.7562	-0.0583	0.061	-14.4738	-14.4652	78.5382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 182
2	X-RAY DIFFRACTION	2	B	3 - 179
3	X-RAY DIFFRACTION	3	C	3 - 179
4	X-RAY DIFFRACTION	4	D	3 - 179
5	X-RAY DIFFRACTION	5	E	3 - 179
6	X-RAY DIFFRACTION	6	F	3 - 181
7	X-RAY DIFFRACTION	7	G	3 - 179
8	X-RAY DIFFRACTION	8	H	3 - 177

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