PDB-2jas: Structure of deoxyadenosine kinase from M.mycoides with bound dATP

ID or keywords:

Entry

Database: PDB / ID: 2jas

Title

Structure of deoxyadenosine kinase from M.mycoides with bound dATP

Components

DEOXYGUANOSINE KINASE

Keywords

TRANSFERASE / KINASE

Function / homology

Function and homology information

deoxyguanosine kinase / deoxyguanosine kinase activity / ATP binding / cytoplasm
Similarity search - Function

Biological species

MYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Welin, M. / Wang, L. / Eriksson, S. / Eklund, H.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Structure-Function Analysis of a Bacterial Deoxyadenosine Kinase Reveals the Basis for Substrate Specificity.
Authors: Welin, M. / Wang, L. / Eriksson, S. / Eklund, H.

History

Deposition	Nov 30, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	2jas.cif.gz	247.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2jas.ent.gz	200.4 KB	Display	PDB format
PDBx/mmJSON format	2jas.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2jas_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	2jas_full_validation.pdf.gz	2.2 MB	Display
Data in XML	2jas_validation.xml.gz	42.2 KB	Display
Data in CIF	2jas_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ja/2jas ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jas	HTTPS FTP

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Related structure data

Related structure data	2jaqC 2jatC 1p5zS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3mwk-d 2qkk-4 2nrh-d 2oxe-2 4tmk-3 4hd5-d 3mwj-d 3uxm-6 3uwk-3 3hjn-d 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

2jaqC

2jatC

1p5zS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: DEOXYGUANOSINE KINASE

B: DEOXYGUANOSINE KINASE

C: DEOXYGUANOSINE KINASE

D: DEOXYGUANOSINE KINASE

E: DEOXYGUANOSINE KINASE

F: DEOXYGUANOSINE KINASE

hetero molecules

150 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DEOXYGUANOSINE KINASE

B: DEOXYGUANOSINE KINASE

hetero molecules

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

2

C: DEOXYGUANOSINE KINASE

D: DEOXYGUANOSINE KINASE

hetero molecules

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

3

E: DEOXYGUANOSINE KINASE

F: DEOXYGUANOSINE KINASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	190.845, 100.850, 109.486
Angle α, β, γ (deg.)	90.00, 124.58, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ALA	ALA	A	A	1 - 18	2 - 19
2	1	MET	MET	ALA	ALA	B	B	1 - 18	2 - 19
3	1	MET	MET	ALA	ALA	C	C	1 - 18	2 - 19
4	1	MET	MET	ALA	ALA	D	D	1 - 18	2 - 19
5	1	MET	MET	ALA	ALA	E	E	1 - 18	2 - 19
6	1	MET	MET	ALA	ALA	F	F	1 - 18	2 - 19
1	2	GLU	GLU	ASP	ASP	A	A	35 - 45	36 - 46
2	2	GLU	GLU	ASP	ASP	B	B	35 - 45	36 - 46
3	2	GLU	GLU	ASP	ASP	C	C	35 - 45	36 - 46
4	2	GLU	GLU	ASP	ASP	D	D	35 - 45	36 - 46
5	2	GLU	GLU	ASP	ASP	E	E	35 - 45	36 - 46
6	2	GLU	GLU	ASP	ASP	F	F	35 - 45	36 - 46
1	3	LYS	LYS	LYS	LYS	A	A	48 - 52	49 - 53
2	3	LYS	LYS	LYS	LYS	B	B	48 - 52	49 - 53
3	3	LYS	LYS	LYS	LYS	C	C	48 - 52	49 - 53
4	3	LYS	LYS	LYS	LYS	D	D	48 - 52	49 - 53
5	3	LYS	LYS	LYS	LYS	E	E	48 - 52	49 - 53
6	3	LYS	LYS	LYS	LYS	F	F	48 - 52	49 - 53
1	4	TYR	TYR	LEU	LEU	A	A	56 - 65	57 - 66
2	4	TYR	TYR	LEU	LEU	B	B	56 - 65	57 - 66
3	4	TYR	TYR	LEU	LEU	C	C	56 - 65	57 - 66
4	4	TYR	TYR	LEU	LEU	D	D	56 - 65	57 - 66
5	4	TYR	TYR	LEU	LEU	E	E	56 - 65	57 - 66
6	4	TYR	TYR	LEU	LEU	F	F	56 - 65	57 - 66
1	5	PHE	PHE	PHE	PHE	A	A	76 - 107	77 - 108
2	5	PHE	PHE	PHE	PHE	B	B	76 - 107	77 - 108
3	5	PHE	PHE	PHE	PHE	C	C	76 - 107	77 - 108
4	5	PHE	PHE	PHE	PHE	D	D	76 - 107	77 - 108
5	5	PHE	PHE	PHE	PHE	E	E	76 - 107	77 - 108
6	5	PHE	PHE	PHE	PHE	F	F	76 - 107	77 - 108
1	6	ILE	ILE	ILE	ILE	A	A	127 - 142	128 - 143
2	6	ILE	ILE	ILE	ILE	B	B	127 - 142	128 - 143
3	6	ILE	ILE	ILE	ILE	C	C	127 - 142	128 - 143
4	6	ILE	ILE	ILE	ILE	D	D	127 - 142	128 - 143
5	6	ILE	ILE	ILE	ILE	E	E	127 - 142	128 - 143
6	6	ILE	ILE	ILE	ILE	F	F	127 - 142	128 - 143
1	7	SER	SER	SER	SER	A	A	148 - 200	149 - 201
2	7	SER	SER	SER	SER	B	B	148 - 200	149 - 201
3	7	SER	SER	SER	SER	C	C	148 - 200	149 - 201
4	7	SER	SER	SER	SER	D	D	148 - 200	149 - 201
5	7	SER	SER	SER	SER	E	E	148 - 200	149 - 201
6	7	SER	SER	SER	SER	F	F	148 - 200	149 - 201

NCS oper: (Code: given
Matrix: (-0.5549, 0.8211, 0.134), (0.8242, 0.5206, 0.2229), (0.1132, 0.2341, -0.9656)
Vector: -111.1, 52.82, 51.2)

#1: Protein	DEOXYGUANOSINE KINASE / DEOXYRIBONUCLEOSIDE KINASE Mass: 24427.000 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOPLASMA MYCOIDES SUBSP. MYCOIDES SC (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93IG4, deoxyguanosine kinase
#2: Chemical	ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.9 Å³/Da / Density % sol: 57 %
Crystal grow	pH: 7 / Details: 24% PEG 3350 0.2 M KSCN, pH 7.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 25, 2004 / Details: MIRROR
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.1 Å / Num. obs: 46941 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / R_merge(I) obs: 0.08 / Net I/σ(I): 15.6
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5Z

1p5z

Resolution: 2.7→47 Å / Cor.coef. F_o:F_c: 0.913 / Cor.coef. F_o:F_c free: 0.886 / SU B: 28.032 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.914 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 115-122 ARE DISORDERED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	2372	5.1 %	RANDOM
R_work	0.233	-	-	-
obs	0.235	44555	99.7 %	-

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: 40.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.26 Å²	0 Å²	-0.53 Å²
2-	-	2.2 Å²	0 Å²
3-	-	-	-1.55 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9715	0	186	16	9917

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	10089
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.143	1.989	13628
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.14	5	1149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.548	25.336	506
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.323	15	1909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.863	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1492
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7410
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	4363
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	6915
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	303
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	0.198	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.104	0.2	12
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	0.301	1.5	5913
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.536	2	9420
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.654	3	4759
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.058	4.5	4208
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1213 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.37	0.5
2	B	medium positional	0.38	0.5
3	C	medium positional	0.41	0.5
4	D	medium positional	0.31	0.5
5	E	medium positional	0.31	0.5
6	F	medium positional	0.37	0.5
1	A	medium thermal	0.29	2
2	B	medium thermal	0.27	2
3	C	medium thermal	0.34	2
4	D	medium thermal	0.17	2
5	E	medium thermal	0.17	2
6	F	medium thermal	0.29	2

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.42	173
R_work	0.324	3279

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	3.3978	-1.4825	1.0704	3.3213	-2.1268	3.9256	-0.197	0.2696	0.1616	0.0247	0.0403	-0.1815	-0.3225	0.1539	0.1566	-0.0366	0.1219	-0.0112	0.1018	0.1209	-0.1	-51.38	10.8	39.569
2	3.7826	-1.2068	0.8648	2.5165	-1.8529	5.7875	0.0473	-0.0454	-0.3363	0.0106	-0.0471	0.2398	0.2662	-0.3607	-0.0001	0.0278	0.2215	0.0561	0.1146	0.1735	-0.0483	-69.066	24.486	9.897
3	4.2175	-1.8833	-1.0117	2.5648	-0.989	2.6708	-0.1091	-0.0038	-0.4394	-0.3224	0.0718	0.2623	0.2939	-0.0744	0.0373	-0.0529	0.0739	-0.0295	-0.0943	0.0702	-0.0758	-60.74	33.169	-23.282
4	8.6553	-2.3007	-1.4088	1.0092	-0.3406	1.5154	-0.1507	-0.4826	-0.4621	0.207	0.2517	0.2932	0.0235	-0.2098	-0.1011	0.1046	0.2022	-0.0234	0.1708	0.1094	0.0512	-92.329	50.543	-17.775
5	3.2621	-1.3397	-3.2119	1.4493	0.1212	7.1393	0.2033	0.4799	0.3179	-0.139	-0.0824	0.1894	-0.2644	-0.6931	-0.1208	0.0052	0.2129	0.0879	0.1801	0.2687	0.1516	-20.129	19.42	-35.918
6	3.1048	0.3678	-1.252	2.6128	-2.5775	3.8821	0.0195	-0.3141	-0.3549	-0.0882	-0.124	-0.1057	0.3177	0.2449	0.1046	0.0082	0.193	0.0361	0.2442	0.1145	0.0325	-40.385	12.577	-5.338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 115
2	X-RAY DIFFRACTION	1	A	124 - 200
3	X-RAY DIFFRACTION	2	B	1 - 115
4	X-RAY DIFFRACTION	2	B	124 - 200
5	X-RAY DIFFRACTION	3	C	1 - 116
6	X-RAY DIFFRACTION	3	C	123 - 200
7	X-RAY DIFFRACTION	4	D	1 - 116
8	X-RAY DIFFRACTION	4	D	125 - 200
9	X-RAY DIFFRACTION	5	E	1 - 116
10	X-RAY DIFFRACTION	5	E	123 - 200
11	X-RAY DIFFRACTION	6	F	1 - 115
12	X-RAY DIFFRACTION	6	F	125 - 200

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