PDB-4x9e: DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE from Escherichia c...

ID or keywords:

Entry

Database: PDB / ID: 4x9e

Title

DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE from Escherichia coli with two DNA effector molecules

Components

Deoxyguanosinetriphosphate triphosphohydrolase
RNA (5'-R(P*CP*CP*C)-3')

Keywords

HYDROLASE/DNA / TRIPHOSPHOHYDROLASE / HYDROLASE-DNA complex

Function / homology

Function and homology information

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 / Resolution: 3.1 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 11, 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 / entity_src_nat / pdbx_struct_oper_list 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 / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4x9e.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4x9e.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4x9e.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x9/4x9e ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x9e	HTTPS FTP

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Related structure data

Related structure data	4xdsC C: citing same article (ref.)
Similar structure data	6oiv-d 6oiy-d 4xds-d 6oiw-d 6oi7-d 6oix-d 1fui-d 4c21-1 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

G: RNA (5'-R(P*CP*CP*C)-3')

H: RNA (5'-R(P*CP*CP*C)-3')

hetero molecules

359 kDa, 8 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)	136.800, 159.800, 190.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	((chain A and (not ( (( resid 17 or resid...
2	1	1	((chain B and (not ( (( resid 17 or resid...
1	1	2	(chain C and (not ( (( resid 17 or resid...
2	1	2	(chain D and (not ( (( resid 17 or resid...
3	1	2	(chain E and (not ( (( resid 17 or resid...
4	1	2	(chain F and (not ( (( resid 17 or resid...
1	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
2	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
3	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
4	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
5	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
6	1	3	((resid 5:15 or resid 18:32 or resid 39:52 or resid...
1	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...
2	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...
3	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...
4	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...
5	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...
6	1	4	((resid 289:315 or resid 333:349 or resid 351:392 or resid...

NCS ensembles :

ID
1
2
3
4

#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 (E. coli) / Strain: K12 / Gene: dgt, b0160, JW0156 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15723, dGTPase
#2: RNA chain	RNA (5'-R(PCPCPC)-3') Mass: 870.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: The DNA model represents an uknown heterogeneous sequence. Source: (natural) Escherichia coli* (E. coli) Plasmid details: Random fragments of nuclease-treated host DNA
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.53 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein solution (10 mg/mL dGTPase, 20 mM Tris-HCl, pH 7.0) mixed 1:1 with well solution (0.1 M sodium acetate, 8% w/v polyethylene glycol 4000, pH 4.6). Cryo conditions are well solution at 25% ethylene glycol.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2007
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 76093 / % possible obs: 99.9 % / Redundancy: 6 % / Net I/σ(I): 15.1
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.725 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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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

Resolution: 3.1→49.632 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2229	3874	5.11 %	Random selection
R_work	0.1669	-	-	-
obs	0.1697	75861	99.66 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→49.632 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24358	111	2	0	24471

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	25084
X-RAY DIFFRACTION	f_angle_d	1.173	33991
X-RAY DIFFRACTION	f_dihedral_angle_d	15.92	9295
X-RAY DIFFRACTION	f_chiral_restr	0.042	3670
X-RAY DIFFRACTION	f_plane_restr	0.006	4342

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3766	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3766	X-RAY DIFFRACTION	POSITIONAL	0.032
2	1	C	3743	X-RAY DIFFRACTION	POSITIONAL
2	2	D	3743	X-RAY DIFFRACTION	POSITIONAL	0.046
2	3	E	3767	X-RAY DIFFRACTION	POSITIONAL	0.05
2	4	F	3737	X-RAY DIFFRACTION	POSITIONAL	0.042
3	1	A	937	X-RAY DIFFRACTION	POSITIONAL
3	2	B	937	X-RAY DIFFRACTION	POSITIONAL	0.022
3	3	C	948	X-RAY DIFFRACTION	POSITIONAL	0.051
3	4	D	942	X-RAY DIFFRACTION	POSITIONAL	0.046
3	5	E	950	X-RAY DIFFRACTION	POSITIONAL	0.049
3	6	F	941	X-RAY DIFFRACTION	POSITIONAL	0.046
4	1	A	1425	X-RAY DIFFRACTION	POSITIONAL
4	2	B	1425	X-RAY DIFFRACTION	POSITIONAL	0.027
4	3	C	1446	X-RAY DIFFRACTION	POSITIONAL	0.069
4	4	D	1439	X-RAY DIFFRACTION	POSITIONAL	0.054
4	5	E	1448	X-RAY DIFFRACTION	POSITIONAL	0.058
4	6	F	1427	X-RAY DIFFRACTION	POSITIONAL	0.056

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 (%)
3.1-3.1378	0.3875	145	0.2678	2369	X-RAY DIFFRACTION	94
3.1378-3.1775	0.3397	141	0.2612	2548	X-RAY DIFFRACTION	100
3.1775-3.2193	0.3998	125	0.2439	2572	X-RAY DIFFRACTION	100
3.2193-3.2634	0.2851	144	0.223	2528	X-RAY DIFFRACTION	100
3.2634-3.31	0.2889	137	0.207	2506	X-RAY DIFFRACTION	100
3.31-3.3594	0.2698	145	0.2007	2548	X-RAY DIFFRACTION	100
3.3594-3.4119	0.3032	147	0.2113	2563	X-RAY DIFFRACTION	100
3.4119-3.4678	0.27	154	0.2006	2522	X-RAY DIFFRACTION	100
3.4678-3.5276	0.2787	137	0.1899	2545	X-RAY DIFFRACTION	100
3.5276-3.5917	0.2809	122	0.1858	2568	X-RAY DIFFRACTION	100
3.5917-3.6608	0.2611	128	0.1758	2575	X-RAY DIFFRACTION	100
3.6608-3.7355	0.2006	153	0.1664	2542	X-RAY DIFFRACTION	100
3.7355-3.8167	0.2262	116	0.1601	2591	X-RAY DIFFRACTION	100
3.8167-3.9055	0.2096	142	0.1505	2548	X-RAY DIFFRACTION	100
3.9055-4.0031	0.2203	143	0.1561	2560	X-RAY DIFFRACTION	100
4.0031-4.1113	0.2142	142	0.1469	2566	X-RAY DIFFRACTION	100
4.1113-4.2322	0.2205	130	0.1424	2557	X-RAY DIFFRACTION	100
4.2322-4.3687	0.1861	127	0.1355	2564	X-RAY DIFFRACTION	100
4.3687-4.5247	0.1804	142	0.1286	2591	X-RAY DIFFRACTION	100
4.5247-4.7058	0.186	128	0.1345	2592	X-RAY DIFFRACTION	100
4.7058-4.9198	0.2004	122	0.132	2573	X-RAY DIFFRACTION	100
4.9198-5.1789	0.1917	134	0.1438	2603	X-RAY DIFFRACTION	100
5.1789-5.503	0.2275	131	0.1566	2611	X-RAY DIFFRACTION	100
5.503-5.9272	0.2308	129	0.1599	2615	X-RAY DIFFRACTION	100
5.9272-6.5225	0.2143	139	0.1714	2617	X-RAY DIFFRACTION	100
6.5225-7.4636	0.2047	144	0.1727	2620	X-RAY DIFFRACTION	100
7.4636-9.3929	0.1805	153	0.1571	2659	X-RAY DIFFRACTION	100
9.3929-49.6386	0.2262	174	0.1968	2734	X-RAY DIFFRACTION	99

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	1.532	-0.0832	0.885	1.3634	-0.2561	2.3522	0.0196	-0.5196	-0.0318	0.4136	-0.103	-0.0109	0.0146	-0.128	0.0817	1.0623	-0.0298	0.0995	0.7385	-0.0187	0.5569	1.9746	-42.1275	-20.6086
2	2.1932	1.8713	-0.3323	2.3518	-0.2471	0.7386	0.1189	-0.374	-0.6764	0.3057	-0.1902	-0.588	0.3388	0.2709	0.0757	1.1696	0.1941	-0.0443	0.8135	0.172	0.8108	34.0451	-56.3211	-24.7691
3	1.2945	-0.6367	-0.185	2.4917	0.8409	1.7996	-0.0579	0.1841	-0.0885	-0.1948	-0.0904	0.1852	0.0832	-0.0838	0.1432	0.6556	-0.0871	0.0587	0.5327	0.0112	0.4623	4.4086	-28.8101	-74.6853
4	1.3953	-0.1887	0.8321	1.8988	-0.9715	6.2501	0.003	0.1005	-0.0218	-0.4522	-0.1883	-0.3797	0.8628	1.035	0.1373	0.9142	0.1621	0.2061	0.7475	0.0429	0.6525	39.2115	-36.4218	-76.145
5	1.9611	0.7997	-0.5007	1.7725	-0.2615	0.9052	0.0145	0.0685	0.0982	0.0403	0.0302	-0.1039	-0.1117	0.0334	-0.0353	0.7346	0.0028	-0.0833	0.5517	-0.0549	0.4478	18.0751	7.8572	-36.9461
6	0.9787	-0.174	-0.1701	4.0119	2.5756	4.1822	0.0322	-0.322	0.0005	0.1558	0.196	-0.4152	-0.1619	0.9605	-0.1935	0.6262	-0.1391	-0.0275	0.9688	0.0116	0.571	51.573	-4.5009	-33.6227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A or chain G
2	X-RAY DIFFRACTION	2	chain B or chain H
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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