PDB-4xds: Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia c...

ID or keywords:

Entry

Database: PDB / ID: 4xds

Title

Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel

Components

Deoxyguanosinetriphosphate triphosphohydrolase

Keywords

HYDROLASE/DNA / TRIPHOSPHOHYDROLASE / HYDROLASE-DNA complex

Function / homology

Function and homology information

pyrimidine deoxyribonucleoside salvage / dGTPase / dGTPase activity / dGTP catabolic process / nucleobase-containing small molecule interconversion / cobalt ion binding / single-stranded DNA binding / manganese ion binding / GTPase activity / magnesium ion binding / identical protein binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.354 Å

Authors

Singh, D. / Gawel, D. / Itsko, M. / Krahn, J.M. / London, R.E. / Schaaper, R.M.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Structure of Escherichia coli dGTP Triphosphohydrolase: A HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES.
Authors: Singh, D. / Gawel, D. / Itsko, M. / Hochkoeppler, A. / Krahn, J.M. / London, R.E. / Schaaper, R.M.

History

Deposition	Dec 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Apr 29, 2015	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xds.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4xds.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4xds.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4xds_validation.pdf.gz	516.4 KB	Display	wwPDB validaton report
Full document	4xds_full_validation.pdf.gz	555.4 KB	Display
Data in XML	4xds_validation.xml.gz	100 KB	Display
Data in CIF	4xds_validation.cif.gz	132 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/4xds ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xds	HTTPS FTP

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Related structure data

Related structure data	4x9eC C: citing same article (ref.)
Similar structure data	6oiy-d 4x9e-d 6oi7-d 6oix-d 6oiv-d 6oiw-d 1fui-d 6k1g-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

A: Deoxyguanosinetriphosphate triphosphohydrolase

B: Deoxyguanosinetriphosphate triphosphohydrolase

C: Deoxyguanosinetriphosphate triphosphohydrolase

D: Deoxyguanosinetriphosphate triphosphohydrolase

E: Deoxyguanosinetriphosphate triphosphohydrolase

F: Deoxyguanosinetriphosphate triphosphohydrolase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	189.800, 189.800, 296.800
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	(chain C and (resid 1000:1004 or resid 1007 or resid...
2	1	1	(chain A and (resid 1000:1004 or resid 1007 or resid...
3	1	1	(chain B and (resid 1000:1004 or resid 1007 or resid...
4	1	1	(chain D and (resid 1000:1004 or resid 1007 or resid...
5	1	1	(chain E and (resid 1000:1004 or resid 1007 or resid...
6	1	1	(chain F and (resid 1000:1004 or resid 1007 or resid...
1	1	2	(chain C and (resid 4:11 or resid 80:110 or resid...
2	1	2	(chain A and (resid 4:11 or resid 80:110 or resid...
3	1	2	(chain B and (resid 4:11 or resid 80:110 or resid...
4	1	2	(chain D and (resid 4:11 or resid 80:110 or resid...
5	1	2	(chain E and (resid 4:11 or resid 80:110 or resid...
6	1	2	(chain F and (resid 4:11 or resid 80:110 or resid...
1	1	3	(chain D and (resid 122:257 or resid 1008))
2	1	3	(chain A and (resid 122:257 or resid 1008))
3	1	3	(chain B and (resid 122:257 or resid 1008))
4	1	3	(chain C and (resid 122:257 or resid 1008))
5	1	3	(chain E and (resid 122:257 or resid 1008))
6	1	3	(chain F and (resid 122:257 or resid 1008))
1	1	4	(chain C and (resid 258:270 or resid 341:393) and not...
2	1	4	(chain A and (resid 258:270 or resid 341:393) and not...
3	1	4	(chain B and (resid 258:270 or resid 341:393) and not...
4	1	4	(chain D and (resid 258:270 or resid 341:393) and not...
5	1	4	(chain E and (resid 258:270 or resid 341:393) and not...
6	1	4	(chain F and (resid 258:270 or resid 341:393) and not...
1	1	5	(chain C and (resid 274:340) and not ((resid 317:318 or...
2	1	5	(chain A and (resid 274:340) and not ((resid 317:318 or...
3	1	5	(chain B and (resid 274:340) and not ((resid 317:318 or...
4	1	5	(chain D and (resid 274:340) and not ((resid 317:318 or...
5	1	5	(chain E and (resid 274:340) and not ((resid 317:318 or...
6	1	5	(chain F and (resid 274:340) and not ((resid 317:318 or...
1	1	6	(chain C and (resid 394:505 or resid 1005:1006 or resid...
2	1	6	(chain A and (resid 394:505 or resid 1005:1006 or resid...
3	1	6	(chain B and (resid 394:505 or resid 1005:1006 or resid...
4	1	6	(chain D and (resid 394:505 or resid 1005:1006 or resid...
5	1	6	(chain E and (resid 394:505 or resid 1005:1006 or resid...
6	1	6	(chain F and (resid 394:505 or resid 1005:1006 or resid...

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Deoxyguanosinetriphosphate triphosphohydrolase / dGTPase Mass: 59470.863 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dgt, b0160, JW0156 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15723, dGTPase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 67.64 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution ...Details: Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution mixed with 25% ethylene glycol.

Crystal

Density Matthews: 3.8 Å³/Da / Density % sol: 67.64 %

Crystal grow

Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.35→20 Å / Num. obs: 76628 / % possible obs: 98.6 % / Redundancy: 6.2 % / R_merge(I) obs: 0.147 / Net I/σ(I): 8.1
Reflection shell	Resolution: 3.35→3.47 Å / Redundancy: 5 % / R_merge(I) obs: 0.699 / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.354→19.99 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2088	3404	5.14 %
R_work	0.172	-	-
obs	0.1739	66200	85.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.354→19.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24119	0	401	18	24538

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	25067
X-RAY DIFFRACTION	f_angle_d	1.242	34056
X-RAY DIFFRACTION	f_dihedral_angle_d	15.717	9072
X-RAY DIFFRACTION	f_chiral_restr	0.044	3638
X-RAY DIFFRACTION	f_plane_restr	0.005	4304

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	624	X-RAY DIFFRACTION	POSITIONAL
1	2	A	624	X-RAY DIFFRACTION	POSITIONAL	0.049
1	3	B	618	X-RAY DIFFRACTION	POSITIONAL	0.046
1	4	D	634	X-RAY DIFFRACTION	POSITIONAL	0.056
1	5	E	640	X-RAY DIFFRACTION	POSITIONAL	0.056
1	6	F	631	X-RAY DIFFRACTION	POSITIONAL	0.054
2	1	C	286	X-RAY DIFFRACTION	POSITIONAL
2	2	A	286	X-RAY DIFFRACTION	POSITIONAL	0.046
2	3	B	285	X-RAY DIFFRACTION	POSITIONAL	0.044
2	4	D	300	X-RAY DIFFRACTION	POSITIONAL	0.06
2	5	E	310	X-RAY DIFFRACTION	POSITIONAL	0.052
2	6	F	307	X-RAY DIFFRACTION	POSITIONAL	0.058
3	1	D	1093	X-RAY DIFFRACTION	POSITIONAL
3	2	A	1093	X-RAY DIFFRACTION	POSITIONAL	0.045
3	3	B	1106	X-RAY DIFFRACTION	POSITIONAL	0.043
3	4	C	1099	X-RAY DIFFRACTION	POSITIONAL	0.045
3	5	E	1115	X-RAY DIFFRACTION	POSITIONAL	0.045
3	6	F	1101	X-RAY DIFFRACTION	POSITIONAL	0.052
4	1	C	516	X-RAY DIFFRACTION	POSITIONAL
4	2	A	516	X-RAY DIFFRACTION	POSITIONAL	0.046
4	3	B	521	X-RAY DIFFRACTION	POSITIONAL	0.041
4	4	D	517	X-RAY DIFFRACTION	POSITIONAL	0.05
4	5	E	517	X-RAY DIFFRACTION	POSITIONAL	0.046
4	6	F	518	X-RAY DIFFRACTION	POSITIONAL	0.047
5	1	C	439	X-RAY DIFFRACTION	POSITIONAL
5	2	A	439	X-RAY DIFFRACTION	POSITIONAL	0.039
5	3	B	442	X-RAY DIFFRACTION	POSITIONAL	0.036
5	4	D	446	X-RAY DIFFRACTION	POSITIONAL	0.04
5	5	E	485	X-RAY DIFFRACTION	POSITIONAL	0.043
5	6	F	456	X-RAY DIFFRACTION	POSITIONAL	0.042
6	1	C	933	X-RAY DIFFRACTION	POSITIONAL
6	2	A	933	X-RAY DIFFRACTION	POSITIONAL	0.045
6	3	B	929	X-RAY DIFFRACTION	POSITIONAL	0.045
6	4	D	930	X-RAY DIFFRACTION	POSITIONAL	0.05
6	5	E	927	X-RAY DIFFRACTION	POSITIONAL	0.045
6	6	F	929	X-RAY DIFFRACTION	POSITIONAL	0.045

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 (%)
3.3535-3.4728	0.3015	296	0.2667	5547	X-RAY DIFFRACTION	76
3.4728-3.611	0.2761	323	0.2326	5678	X-RAY DIFFRACTION	79
3.611-3.7744	0.2509	331	0.205	5822	X-RAY DIFFRACTION	80
3.7744-3.9719	0.2285	287	0.1905	5907	X-RAY DIFFRACTION	80
3.9719-4.2185	0.2215	321	0.1701	6038	X-RAY DIFFRACTION	82
4.2185-4.5407	0.1906	302	0.1456	6211	X-RAY DIFFRACTION	84
4.5407-4.9912	0.1783	360	0.1361	6460	X-RAY DIFFRACTION	88
4.9912-5.6988	0.1998	366	0.1538	6682	X-RAY DIFFRACTION	90
5.6988-7.1254	0.21	404	0.1763	7015	X-RAY DIFFRACTION	94
7.1254-19.99	0.1801	414	0.162	7436	X-RAY DIFFRACTION	96

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	2.8299	1.0487	-0.1081	2.5553	0.3412	1.6109	0.0645	0.4689	-0.2191	-0.8593	0.1862	-0.7569	-0.0839	0.6081	-0.2082	1.1218	0.2212	0.3719	1.2811	0.0226	0.8383	71.7315	-36.1126	-13.1933
2	1.3126	0.2635	-0.1158	2.6859	-0.0451	3.5652	-0.0423	0.297	0.2861	-0.7922	-0.0275	-0.3852	-0.7511	0.5185	0.0445	0.8749	-0.0778	0.1545	0.9109	0.1488	0.7776	67.8905	-4.8862	3.7473
3	2.6843	-0.6741	0.5633	1.648	-0.5978	1.5115	0.1503	0.4329	-0.1571	-0.3585	-0.1192	-0.0156	0.263	0.2959	-0.0191	0.5711	0.0926	-0.0738	0.6137	-0.0246	0.5226	18.6974	-43.9682	-4.0231
4	3.5631	0.619	0.388	1.4953	-0.1563	1.2443	0.0884	-0.0464	0.3065	0.1813	-0.0805	0.0588	-0.0296	0.1597	0.0075	0.4901	0.0102	-0.0321	0.4806	0.0861	0.5349	17.3574	-16.2242	17.9481
5	1.2471	-0.186	-0.5332	1.393	-0.5765	3.4344	0.1122	0.3581	-0.1441	-0.2384	-0.122	0.1822	0.3628	-0.1523	0.0102	0.4917	0.0755	-0.0508	0.5819	0.016	0.5831	55.9179	-64.759	29.8479
6	1.9703	-0.7687	0.3376	2.0391	-0.8252	1.738	-0.0478	-0.0969	0.3047	-0.0115	0.0384	-0.1208	-0.1554	0.2104	-0.0019	0.4096	-0.0593	0.0088	0.4656	0.0025	0.4989	58.0956	-34.8484	48.3606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F

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