PDB-1zmx: Crystal structure of D. melanogaster deoxyribonucleoside kinase N...

ID or keywords:

Entry

Database: PDB / ID: 1zmx

Title

Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine

Components

Deoxynucleoside kinase

Keywords

TRANSFERASE / Drosophila melanogaster / dnk / N64D mutant

Function / homology

Function and homology information

deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / uridine kinase activity / nucleoside salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / thymidine kinase activity / deoxyadenosine kinase activity ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Welin, M. / Skovgaard, T. / Knecht, W. / Berenstein, D. / Munch-Petersen, B. / Piskur, J. / Eklund, H.

Citation

Journal: Febs J. / Year: 2005
Title: Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D.
Authors: Welin, M. / Skovgaard, T. / Knecht, W. / Zhu, C. / Berenstein, D. / Munch-Petersen, B. / Piskur, J. / Eklund, H.

History

Deposition	May 11, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 24, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 20, 2021	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation Category: chem_comp / database_2 ...chem_comp / database_2 / exptl_crystal_grow / struct_ref_seq_dif / struct_site Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 23, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1zmx.cif.gz	319.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1zmx.ent.gz	260.1 KB	Display	PDB format
PDBx/mmJSON format	1zmx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1zmx_validation.pdf.gz	522.8 KB	Display	wwPDB validaton report
Full document	1zmx_full_validation.pdf.gz	551.3 KB	Display
Data in XML	1zmx_validation.xml.gz	55 KB	Display
Data in CIF	1zmx_validation.cif.gz	67 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/1zmx ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zmx	HTTPS FTP

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Related structure data

Related structure data	1zm7C 1ot3S 1j90 1oe0 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2jj8-1 2vp6-2 2vp9-2 2jj8-2 2vp5-d 1ot3-3 2vp6-3 2vp9-1 2vqs-2 1ot3-2 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) 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Deoxynucleoside kinase

B: Deoxynucleoside kinase

C: Deoxynucleoside kinase

D: Deoxynucleoside kinase

E: Deoxynucleoside kinase

F: Deoxynucleoside kinase

G: Deoxynucleoside kinase

H: Deoxynucleoside kinase

hetero molecules

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

1

A: Deoxynucleoside kinase

B: Deoxynucleoside kinase

hetero molecules

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

2

C: Deoxynucleoside kinase

D: Deoxynucleoside kinase

hetero molecules

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

3

E: Deoxynucleoside kinase

F: Deoxynucleoside kinase

hetero molecules

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

4

G: Deoxynucleoside kinase

H: Deoxynucleoside kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.712, 70.340, 224.528
Angle α, β, γ (deg.)	90.00, 90.69, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	VAL	VAL	1	A	A	12 - 54	12 - 54
2	1	THR	THR	VAL	VAL	1	B	B	12 - 54	12 - 54
3	1	THR	THR	VAL	VAL	1	C	C	12 - 54	12 - 54
4	1	THR	THR	VAL	VAL	1	D	D	12 - 54	12 - 54
5	1	THR	THR	VAL	VAL	1	E	E	12 - 54	12 - 54
6	1	THR	THR	VAL	VAL	1	F	F	12 - 54	12 - 54
7	1	THR	THR	VAL	VAL	1	G	G	12 - 54	12 - 54
8	1	THR	THR	VAL	VAL	1	H	H	12 - 54	12 - 54
9	2	GLU	GLU	GLU	GLU	3	A	A	55	55
10	2	GLU	GLU	GLU	GLU	3	B	B	55	55
11	2	GLU	GLU	GLU	GLU	3	C	C	55	55
12	2	GLU	GLU	GLU	GLU	3	D	D	55	55
13	2	GLU	GLU	GLU	GLU	3	E	E	55	55
14	2	GLU	GLU	GLU	GLU	3	F	F	55	55
15	2	GLU	GLU	GLU	GLU	3	G	G	55	55
16	2	GLU	GLU	GLU	GLU	3	H	H	55	55
17	3	LYS	LYS	LEU	LEU	1	A	A	56 - 66	56 - 66
18	3	LYS	LYS	LEU	LEU	1	B	B	56 - 66	56 - 66
19	3	LYS	LYS	LEU	LEU	1	C	C	56 - 66	56 - 66
20	3	LYS	LYS	LEU	LEU	1	D	D	56 - 66	56 - 66
21	3	LYS	LYS	LEU	LEU	1	E	E	56 - 66	56 - 66
22	3	LYS	LYS	LEU	LEU	1	F	F	56 - 66	56 - 66
23	3	LYS	LYS	LEU	LEU	1	G	G	56 - 66	56 - 66
24	3	LYS	LYS	LEU	LEU	1	H	H	56 - 66	56 - 66
25	4	GLU	GLU	GLU	GLU	3	A	A	67	67
26	4	GLU	GLU	GLU	GLU	3	B	B	67	67
27	4	GLU	GLU	GLU	GLU	3	C	C	67	67
28	4	GLU	GLU	GLU	GLU	3	D	D	67	67
29	4	GLU	GLU	GLU	GLU	3	E	E	67	67
30	4	GLU	GLU	GLU	GLU	3	F	F	67	67
31	4	GLU	GLU	GLU	GLU	3	G	G	67	67
32	4	GLU	GLU	GLU	GLU	3	H	H	67	67
33	5	LEU	LEU	LEU	LEU	1	A	A	68 - 124	68 - 124
34	5	LEU	LEU	LEU	LEU	1	B	B	68 - 124	68 - 124
35	5	LEU	LEU	LEU	LEU	1	C	C	68 - 124	68 - 124
36	5	LEU	LEU	LEU	LEU	1	D	D	68 - 124	68 - 124
37	5	LEU	LEU	LEU	LEU	1	E	E	68 - 124	68 - 124
38	5	LEU	LEU	LEU	LEU	1	F	F	68 - 124	68 - 124
39	5	LEU	LEU	LEU	LEU	1	G	G	68 - 124	68 - 124
40	5	LEU	LEU	LEU	LEU	1	H	H	68 - 124	68 - 124
41	6	GLU	GLU	GLN	GLN	3	A	A	125 - 126	125 - 126
42	6	GLU	GLU	GLN	GLN	3	B	B	125 - 126	125 - 126
43	6	GLU	GLU	GLN	GLN	3	C	C	125 - 126	125 - 126
44	6	GLU	GLU	GLN	GLN	3	D	D	125 - 126	125 - 126
45	6	GLU	GLU	GLN	GLN	3	E	E	125 - 126	125 - 126
46	6	GLU	GLU	GLN	GLN	3	F	F	125 - 126	125 - 126
47	6	GLU	GLU	GLN	GLN	3	G	G	125 - 126	125 - 126
48	6	GLU	GLU	GLN	GLN	3	H	H	125 - 126	125 - 126
49	7	GLY	GLY	ILE	ILE	1	A	A	127 - 139	127 - 139
50	7	GLY	GLY	ILE	ILE	1	B	B	127 - 139	127 - 139
51	7	GLY	GLY	ILE	ILE	1	C	C	127 - 139	127 - 139
52	7	GLY	GLY	ILE	ILE	1	D	D	127 - 139	127 - 139
53	7	GLY	GLY	ILE	ILE	1	E	E	127 - 139	127 - 139
54	7	GLY	GLY	ILE	ILE	1	F	F	127 - 139	127 - 139
55	7	GLY	GLY	ILE	ILE	1	G	G	127 - 139	127 - 139
56	7	GLY	GLY	ILE	ILE	1	H	H	127 - 139	127 - 139
57	8	GLU	GLU	GLU	GLU	3	A	A	140 - 141	140 - 141
58	8	GLU	GLU	GLU	GLU	3	B	B	140 - 141	140 - 141
59	8	GLU	GLU	GLU	GLU	3	C	C	140 - 141	140 - 141
60	8	GLU	GLU	GLU	GLU	3	D	D	140 - 141	140 - 141
61	8	GLU	GLU	GLU	GLU	3	E	E	140 - 141	140 - 141
62	8	GLU	GLU	GLU	GLU	3	F	F	140 - 141	140 - 141
63	8	GLU	GLU	GLU	GLU	3	G	G	140 - 141	140 - 141
64	8	GLU	GLU	GLU	GLU	3	H	H	140 - 141	140 - 141
65	9	SER	SER	ALA	ALA	1	A	A	142 - 160	142 - 160
66	9	SER	SER	ALA	ALA	1	B	B	142 - 160	142 - 160
67	9	SER	SER	ALA	ALA	1	C	C	142 - 160	142 - 160
68	9	SER	SER	ALA	ALA	1	D	D	142 - 160	142 - 160
69	9	SER	SER	ALA	ALA	1	E	E	142 - 160	142 - 160
70	9	SER	SER	ALA	ALA	1	F	F	142 - 160	142 - 160
71	9	SER	SER	ALA	ALA	1	G	G	142 - 160	142 - 160
72	9	SER	SER	ALA	ALA	1	H	H	142 - 160	142 - 160
73	10	TYR	TYR	GLU	GLU	3	A	A	161 - 162	161 - 162
74	10	TYR	TYR	GLU	GLU	3	B	B	161 - 162	161 - 162
75	10	TYR	TYR	GLU	GLU	3	C	C	161 - 162	161 - 162
76	10	TYR	TYR	GLU	GLU	3	D	D	161 - 162	161 - 162
77	10	TYR	TYR	GLU	GLU	3	E	E	161 - 162	161 - 162
78	10	TYR	TYR	GLU	GLU	3	F	F	161 - 162	161 - 162
79	10	TYR	TYR	GLU	GLU	3	G	G	161 - 162	161 - 162
80	10	TYR	TYR	GLU	GLU	3	H	H	161 - 162	161 - 162
81	11	ARG	ARG	ILE	ILE	1	A	A	163 - 164	163 - 164
82	11	ARG	ARG	ILE	ILE	1	B	B	163 - 164	163 - 164
83	11	ARG	ARG	ILE	ILE	1	C	C	163 - 164	163 - 164
84	11	ARG	ARG	ILE	ILE	1	D	D	163 - 164	163 - 164
85	11	ARG	ARG	ILE	ILE	1	E	E	163 - 164	163 - 164
86	11	ARG	ARG	ILE	ILE	1	F	F	163 - 164	163 - 164
87	11	ARG	ARG	ILE	ILE	1	G	G	163 - 164	163 - 164
88	11	ARG	ARG	ILE	ILE	1	H	H	163 - 164	163 - 164
89	12	ARG	ARG	PRO	PRO	2	A	A	165 - 176	165 - 176
90	12	ARG	ARG	PRO	PRO	2	B	B	165 - 176	165 - 176
91	12	ARG	ARG	PRO	PRO	2	C	C	165 - 176	165 - 176
92	12	ARG	ARG	PRO	PRO	2	D	D	165 - 176	165 - 176
93	12	ARG	ARG	PRO	PRO	2	E	E	165 - 176	165 - 176
94	12	ARG	ARG	PRO	PRO	2	F	F	165 - 176	165 - 176
95	12	ARG	ARG	PRO	PRO	2	G	G	165 - 176	165 - 176
96	12	ARG	ARG	PRO	PRO	2	H	H	165 - 176	165 - 176
97	13	LEU	LEU	GLN	GLN	1	A	A	177 - 194	177 - 194
98	13	LEU	LEU	GLN	GLN	1	B	B	177 - 194	177 - 194
99	13	LEU	LEU	GLN	GLN	1	C	C	177 - 194	177 - 194
100	13	LEU	LEU	GLN	GLN	1	D	D	177 - 194	177 - 194
101	13	LEU	LEU	GLN	GLN	1	E	E	177 - 194	177 - 194
102	13	LEU	LEU	GLN	GLN	1	F	F	177 - 194	177 - 194
103	13	LEU	LEU	GLN	GLN	1	G	G	177 - 194	177 - 194
104	13	LEU	LEU	GLN	GLN	1	H	H	177 - 194	177 - 194
105	14	CYS	CYS	ASP	ASP	1	A	A	200 - 206	200 - 206
106	14	CYS	CYS	ASP	ASP	1	B	B	200 - 206	200 - 206
107	14	CYS	CYS	ASP	ASP	1	C	C	200 - 206	200 - 206
108	14	CYS	CYS	ASP	ASP	1	D	D	200 - 206	200 - 206
109	14	CYS	CYS	ASP	ASP	1	E	E	200 - 206	200 - 206
110	14	CYS	CYS	ASP	ASP	1	F	F	200 - 206	200 - 206
111	14	CYS	CYS	ASP	ASP	1	G	G	200 - 206	200 - 206
112	14	CYS	CYS	ASP	ASP	1	H	H	200 - 206	200 - 206

#1: Protein	Deoxynucleoside kinase / Deoxyribonucleoside kinase / Dm-dNK / Multispecific deoxynucleoside kinase Mass: 26907.691 Da / Num. of mol.: 8 / Fragment: residues 1-230 / Mutation: N64D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dnk / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O₅

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 55 %
Crystal grow	Temperature: 288 K / Method: counter-diffusion / pH: 6.5 Details: MES, lithium sulphate, mPEG 2000, pH 6.5, Counter diffusion, temperature 288K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2003 / Details: Mirrors
Radiation	Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 3.1→41.17 Å / Num. obs: 39975 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 39562 / R_sym value: 0.38 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1OT3

1ot3

Resolution: 3.1→41.17 Å / Cor.coef. F_o:F_c: 0.871 / Cor.coef. F_o:F_c free: 0.842 / SU B: 22.712 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2884	2005	5 %	RANDOM
R_work	0.26858	-	-	-
all	0.2696	-	-	-
obs	0.26958	37947	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 37.441 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9 Å²	0 Å²	2.48 Å²
2-	-	2.32 Å²	0 Å²
3-	-	-	-1.36 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→41.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12536	0	176	0	12712

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	13000
X-RAY DIFFRACTION	r_angle_refined_deg	1.134	1.966	17582
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.314	5	1482
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1910
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9688
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	5468
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	304
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.313	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.458	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.635	1.5	7494
X-RAY DIFFRACTION	r_mcangle_it	1.212	2	12184
X-RAY DIFFRACTION	r_scbond_it	1.247	3	5506
X-RAY DIFFRACTION	r_scangle_it	2.254	4.5	5398

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1463	tight positional	0.01	0.01
2	B	1463	tight positional	0.01	0.01
3	C	1463	tight positional	0.01	0.01
4	D	1463	tight positional	0.01	0.01
5	E	1463	tight positional	0.04	0.01
6	F	1463	tight positional	0.01	0.01
7	G	1463	tight positional	0.01	0.01
8	H	1463	tight positional	0.01	0.01
1	A	25	medium positional	0.88	0.5
2	B	25	medium positional	1.14	0.5
3	C	25	medium positional	1.12	0.5
4	D	25	medium positional	0.97	0.5
5	E	25	medium positional	1.91	0.5
6	F	25	medium positional	0.91	0.5
7	G	25	medium positional	1.35	0.5
8	H	25	medium positional	1.09	0.5
1	A	43	loose positional	0.75	5
2	B	43	loose positional	1.05	5
3	C	43	loose positional	1.4	5
4	D	43	loose positional	1.25	5
5	E	43	loose positional	1.05	5
6	F	43	loose positional	1.07	5
7	G	43	loose positional	0.95	5
8	H	43	loose positional	0.96	5
1	A	1463	tight thermal	0.12	0.5
2	B	1463	tight thermal	0.08	0.5
3	C	1463	tight thermal	0.1	0.5
4	D	1463	tight thermal	0.07	0.5
5	E	1463	tight thermal	0.08	0.5
6	F	1463	tight thermal	0.07	0.5
7	G	1463	tight thermal	0.09	0.5
8	H	1463	tight thermal	0.08	0.5
1	A	25	medium thermal	0.3	2
2	B	25	medium thermal	0.61	2
3	C	25	medium thermal	0.48	2
4	D	25	medium thermal	0.34	2
5	E	25	medium thermal	0.65	2
6	F	25	medium thermal	0.46	2
7	G	25	medium thermal	0.47	2
8	H	25	medium thermal	0.98	2
1	A	43	loose thermal	2.47	10
2	B	43	loose thermal	2.84	10
3	C	43	loose thermal	1.64	10
4	D	43	loose thermal	0.85	10
5	E	43	loose thermal	2.83	10
6	F	43	loose thermal	1.83	10
7	G	43	loose thermal	1.69	10
8	H	43	loose thermal	1.5	10

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.302	158
R_work	0.311	2794

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi