PDB-4a6a: A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberc...

ID or keywords:

Entry

Database: PDB / ID: 4a6a

Title

A115V variant of dCTP deaminase-dUTPase from Mycobacterium tuberculosis in complex with dTTP

Components

DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

Keywords

HYDROLASE / DEOXY-RIBONUCLEOTIDE METABOLISM / DTTP INHIBITION

Function / homology

Function and homology information

dCTP deaminase (dUMP-forming) /

dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process /

dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion /

dUTP diphosphatase activity /

nucleotide binding
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.9 Å

Authors

Lovgreen, M.N. / Ucar, E. / Willemoes, M. / Harris, P.

Citation

Journal: To be Published
Title: Dttp Inhibition of the Bifunctional Dctp Deaminase- Dutpase from Mycobacterium Tuberculosis is Ph Dependent: Kinetic Analyses and Crystal Structure of A115V Variant
Authors: Lovgreen, M.N. / Harris, P. / Ucar, E. / Willemoes, M.

History

Deposition	Nov 1, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2012	Group: Structure summary
Revision 1.2	Nov 8, 2017	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	May 8, 2024	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_struct_conn_angle / 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 / _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.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.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_conn.ptnr2_label_seq_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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6a ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6a	HTTPS FTP

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Related structure data

Similar structure data	2v9x-1 1xs1-d 2qlp-d 4doy-2 5x3t-d 2i0b-d 2h7c-3 2v9x-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (4) #238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

B: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

C: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

D: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

E: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

F: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

G: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

H: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

I: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

J: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

K: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

L: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

hetero molecules

257 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

B: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

C: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

D: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

E: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

F: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

hetero molecules

defined by author&software
129 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

H: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

I: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

J: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

K: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

L: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE

hetero molecules

defined by author&software
129 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.590, 179.510, 99.810
Angle α, β, γ (deg.)	90.00, 96.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	H
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	A
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Ens-ID: 1 / Refine code: 1

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	LEU	LEU	H	H	1 - 109	1 - 109
2	1	MET	MET	LEU	LEU	B	B	1 - 109	1 - 109
3	1	MET	MET	LEU	LEU	C	C	1 - 109	1 - 109
4	1	MET	MET	LEU	LEU	D	D	1 - 109	1 - 109
5	1	MET	MET	LEU	LEU	E	E	1 - 109	1 - 109
6	1	MET	MET	LEU	LEU	F	F	1 - 109	1 - 109
7	1	MET	MET	LEU	LEU	G	G	1 - 109	1 - 109
8	1	MET	MET	LEU	LEU	A	A	1 - 109	1 - 109
9	1	MET	MET	LEU	LEU	I	I	1 - 109	1 - 109
10	1	MET	MET	LEU	LEU	J	J	1 - 109	1 - 109
11	1	MET	MET	LEU	LEU	K	K	1 - 109	1 - 109
12	1	MET	MET	LEU	LEU	L	L	1 - 109	1 - 109
1	2	ASP	ASP	ARG	ARG	H	H	119 - 188	119 - 188
2	2	ASP	ASP	ARG	ARG	B	B	119 - 188	119 - 188
3	2	ASP	ASP	ARG	ARG	C	C	119 - 188	119 - 188
4	2	ASP	ASP	ARG	ARG	D	D	119 - 188	119 - 188
5	2	ASP	ASP	ARG	ARG	E	E	119 - 188	119 - 188
6	2	ASP	ASP	ARG	ARG	F	F	119 - 188	119 - 188
7	2	ASP	ASP	ARG	ARG	G	G	119 - 188	119 - 188
8	2	ASP	ASP	ARG	ARG	A	A	119 - 188	119 - 188
9	2	ASP	ASP	ARG	ARG	I	I	119 - 188	119 - 188
10	2	ASP	ASP	ARG	ARG	J	J	119 - 188	119 - 188
11	2	ASP	ASP	ARG	ARG	K	K	119 - 188	119 - 188
12	2	ASP	ASP	ARG	ARG	L	L	119 - 188	119 - 188
1	3	TTP	TTP	MG	MG	H	BA - CA	201 - 202
2	3	TTP	TTP	MG	MG	B	O - P	201 - 202
3	3	TTP	TTP	MG	MG	C	R - S	201 - 202
4	3	TTP	TTP	MG	MG	D	T - U	201 - 202
5	3	TTP	TTP	MG	MG	E	V - W	201 - 202
6	3	TTP	TTP	MG	MG	F	X - Y	201 - 202
7	3	TTP	TTP	MG	MG	G	Z - AA	201 - 202
8	3	TTP	TTP	MG	MG	A	M - N	201 - 202
9	3	TTP	TTP	MG	MG	I	EA - FA	201 - 202
10	3	TTP	TTP	MG	MG	J	GA - HA	201 - 202
11	3	TTP	TTP	MG	MG	K	IA - JA	201 - 202
12	3	TTP	TTP	MG	MG	L	KA - LA	201 - 202

#1: Protein	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / DCTP DEAMINASE / DCTP DEAMNIASE-DUTPASE Mass: 20919.656 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PTBDCD7 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O07247, UniProt: P9WP17*PLUS, dCTP deaminase
#2: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate Mass: 482.168 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.05 Å³/Da / Density % sol: 40 % / Description: NONE
Crystal grow	pH: 7.5 / Details: pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 12, 2010 / Details: FOCUSSING MIRRORS
Radiation	Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9765 Å / Relative weight: 1
Reflection	Resolution: 2.9→99 Å / Num. obs: 43288 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.74 % / R_merge(I) obs: 0.18 / Net I/σ(I): 7.01

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.9→49.42 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.885 / SU B: 52.928 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.564
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28985	2165	5 %	RANDOM
R_work	0.25297	-	-	-
obs	0.25478	41123	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.666 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.45 Å²	0 Å²	-0.05 Å²
2-	-	0.3 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→49.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17538	0	362	12	17912

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	18294
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.613	2.009	24908
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.45	5	2251
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.887	23.182	792
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.347	15	2971
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.318	15	156
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	2767
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	13828
X-RAY DIFFRACTION	r_gen_planes_other
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	0.779	1.5	11255
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.548	2	18224
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.006	3	7039
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.721	4.5	6684
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: 1420 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	H	tight positional	0.05	0.05
2	B	tight positional	0.06	0.05
3	C	tight positional	0.05	0.05
4	D	tight positional	0.05	0.05
5	E	tight positional	0.06	0.05
6	F	tight positional	0.05	0.05
7	G	tight positional	0.05	0.05
8	A	tight positional	0.05	0.05
9	I	tight positional	0.06	0.05
10	J	tight positional	0.05	0.05
11	K	tight positional	0.05	0.05
12	L	tight positional	0.05	0.05
1	H	tight thermal	0.09	0.5
2	B	tight thermal	0.1	0.5
3	C	tight thermal	0.08	0.5
4	D	tight thermal	0.09	0.5
5	E	tight thermal	0.08	0.5
6	F	tight thermal	0.09	0.5
7	G	tight thermal	0.09	0.5
8	A	tight thermal	0.09	0.5
9	I	tight thermal	0.09	0.5
10	J	tight thermal	0.09	0.5
11	K	tight thermal	0.08	0.5
12	L	tight thermal	0.09	0.5

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	162	-
R_work	0.356	3077	-
obs	-	-	100 %

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	0.1919	0.3778	0.2429	1.4879	0.2289	0.5703	0.013	-0.0159	-0.0838	0.1327	0.0121	-0.001	0.1008	-0.0704	-0.0252	0.1228	-0.0045	0.0811	0.1837	-0.0381	0.1997	8.381	-19.505	32.323
2	0.5312	0.3388	0.1809	1.6115	0.4323	0.596	0.0121	-0.0547	0.0008	0.0702	-0.0199	0.055	0.1314	-0.0448	0.0078	0.0535	0.0003	0.0215	0.107	-0.0032	0.065	17.923	23.484	32.173
3	0.588	-0.0939	0.1211	2.2886	-0.1125	0.5941	0.0658	0.128	-0.1461	-0.1088	-0.0733	0.1512	0.0843	-0.0506	0.0076	0.1463	0.0061	-0.0348	0.1876	-0.0404	0.1167	15.426	-21.668	10.113
4	0.6012	0.1681	0.0278	1.9235	0.249	0.3043	0.0282	0.0631	0.0314	-0.1849	-0.0064	-0.0008	-0.0117	-0.0192	-0.0217	0.1203	0.0023	-0.0131	0.1049	0.001	0.0237	22.032	21.981	9.068
5	0.1016	0.4547	-0.0626	2.5699	-0.2311	0.0574	-0.0356	0.0027	-0.0582	0.0301	-0.0155	-0.1177	0.0534	0.0518	0.0511	0.1681	0.0161	-0.0223	0.2265	0.0085	0.2117	30.906	-24.114	27.574
6	0.2349	0.04	0.1485	1.2823	-0.2385	0.7104	0.0048	0.069	-0.0432	-0.0024	0.0265	-0.1839	0.029	0.0889	-0.0314	0.0558	-0.0011	0.0108	0.1135	0.0026	0.141	39.667	18.962	24.367
7	0.2536	0.4655	0.2039	1.3255	0.0634	0.6946	0.0183	-0.0062	-0.0216	0.1125	-0.0327	-0.0269	0.1355	-0.0662	0.0145	0.1162	-0.0141	0.0528	0.1549	-0.0252	0.1524	35.744	70.153	38.041
8	0.6257	0.1426	0.0029	1.0386	0.323	0.8103	-0.0065	-0.1005	0.0309	0.1532	0.0283	0.0615	-0.0273	-0.0223	-0.0219	0.0567	0.0122	0.0116	0.1366	-0.0251	0.0924	45.44	113.145	37.347
9	0.4797	0.108	0.1743	2.4213	-0.0164	0.5119	-0.0127	0.0029	-0.0071	-0.012	-0.0411	0.0766	0.0657	-0.0497	0.0539	0.1124	-0.0115	-0.0108	0.1423	-0.0069	0.0507	42.075	68.02	15.668
10	0.4927	-0.0289	0.1937	1.7402	0.1727	0.5307	0.0322	0.0869	0.0893	-0.1105	-0.0193	-0.0636	-0.1123	-0.0322	-0.0128	0.0884	0.0088	-0.0112	0.1237	-0.0149	0.0651	49.095	111.535	14.295
11	0.3132	0.4984	-0.1314	1.772	-0.1894	0.6183	-0.0458	-0.0266	-0.0484	0.0464	0.0178	-0.1199	0.0742	0.1216	0.028	0.0968	0.0222	-0.0159	0.1873	0.0176	0.1492	58.15	65.445	32.703
12	0.6031	0.4576	0.1207	1.6588	0.1691	1.1611	0.0156	0.0459	0.0349	-0.0114	0.0676	-0.1447	0.0183	0.1234	-0.0832	0.0013	0.001	-0.0017	0.1384	-0.0101	0.1387	67.071	108.484	29.263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 202
2	X-RAY DIFFRACTION	2	B	1 - 202
3	X-RAY DIFFRACTION	3	C	1 - 202
4	X-RAY DIFFRACTION	4	D	1 - 202
5	X-RAY DIFFRACTION	5	E	1 - 202
6	X-RAY DIFFRACTION	6	F	1 - 202
7	X-RAY DIFFRACTION	7	G	1 - 202
8	X-RAY DIFFRACTION	8	H	1 - 202
9	X-RAY DIFFRACTION	9	I	1 - 202
10	X-RAY DIFFRACTION	10	J	1 - 202
11	X-RAY DIFFRACTION	11	K	1 - 202
12	X-RAY DIFFRACTION	12	L	1 - 202

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