PDB-7tu0: Structure of the L. blandensis dGTPase bound to Mn

ID or keywords:

Entry

Database: PDB / ID: 7tu0

Title

Structure of the L. blandensis dGTPase bound to Mn

Components

dGTP triphosphohydrolase

DGTPase

Keywords

HYDROLASE /

dGTPase /

nucleotide binding

Function / homology

Function and homology information

triphosphoric monoester hydrolase activity
Similarity search - Function

Biological species

Leeuwenhoekiella blandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Sikkema, A.P. / Klemm, B.P. / Horng, J.C. / Hall, T.M.T.

Funding support

United States, 1items

Citation

Journal: J Biol Chem / Year: 2022
Title: High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.
Authors: Bradley P Klemm / Andrew P Sikkema / Allen L Hsu / James C Horng / Traci M Tanaka Hall / Mario J Borgnia / Roel M Schaaper /

Abstract: Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to ...

History

Deposition	Feb 2, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 1, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Jul 20, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tu0.cif.gz	554.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7tu0.ent.gz	436.9 KB	Display	PDB format
PDBx/mmJSON format	7tu0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tu/7tu0 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tu0	HTTPS FTP

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Related structure data

Related structure data	26126C 26127C 26128C 26129C 7tu1C 7tu2C 7tu3C 7tu4C 7tu5C 7tu6C 7tu7C 7tu8C 3bg2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: dGTP triphosphohydrolase

B: dGTP triphosphohydrolase

C: dGTP triphosphohydrolase

hetero molecules

159 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: dGTP triphosphohydrolase

B: dGTP triphosphohydrolase

C: dGTP triphosphohydrolase

hetero molecules

A: dGTP triphosphohydrolase

B: dGTP triphosphohydrolase

C: dGTP triphosphohydrolase

hetero molecules

defined by author&software
Evidence: gel filtration, Runs as single peak, approximately homohexamer in size
318 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	181.338, 181.338, 110.606
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	dGTP triphosphohydrolase / DGTPase Mass: 52723.242 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leeuwenhoekiella blandensis (bacteria) / Strain: CECT 7118 / CCUG 51940 / MED217 / Gene: MED217_16760 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3XHN1
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.25 % Description: crystal grew as square bipyramid, approximately 200 microns per side
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystal grown in 1ul:1ul drops of well solution (0.8M Sodium Potassium Tartrate, 0.22M Lithium Sulfate, 0.1M Bis-Tris pH 6.5) and 10mg/mL protein. Cryoprotected by soaking in well solution ...Details: Crystal grown in 1ul:1ul drops of well solution (0.8M Sodium Potassium Tartrate, 0.22M Lithium Sulfate, 0.1M Bis-Tris pH 6.5) and 10mg/mL protein. Cryoprotected by soaking in well solution with 30% ethylene glycol and 1mM MnCl2 added

Crystal

Density Matthews: 3.02 Å³/Da / Density % sol: 59.25 %
Description: crystal grew as square bipyramid, approximately 200 microns per side

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystal grown in 1ul:1ul drops of well solution (0.8M Sodium Potassium Tartrate, 0.22M Lithium Sulfate, 0.1M Bis-Tris pH 6.5) and 10mg/mL protein. Cryoprotected by soaking in well solution ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019 Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation	Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.04→50 Å / Num. obs: 114923 / % possible obs: 100 % / Redundancy: 15.3 % / B_iso Wilson estimate: 47.97 Å² / CC_1/2: 0.999 / CC star: 0.999 / R_merge(I) obs: 0.089 / R_rim(I) all: 0.092 / Net I/σ(I): 17.78
Reflection shell	Resolution: 2.04→2.17 Å / Redundancy: 15.6 % / R_merge(I) obs: 1.66 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 18328 / CC_1/2: 0.669 / CC star: 0.895 / R_rim(I) all: 1.72 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BG2

3bg2

Resolution: 2.04→45.33 Å / SU ML: 0.2813 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2156	3626	1.65 %
R_work	0.191	216797	-
obs	0.1914	114900	98.69 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→45.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10251	0	33	415	10699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	10467
X-RAY DIFFRACTION	f_angle_d	0.8993	14133
X-RAY DIFFRACTION	f_chiral_restr	0.0543	1559
X-RAY DIFFRACTION	f_plane_restr	0.0064	1822
X-RAY DIFFRACTION	f_dihedral_angle_d	15.984	3875

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 (%)
2.04-2.07	0.3814	95	0.3554	5580	X-RAY DIFFRACTION	66.34
2.07-2.1	0.3785	142	0.3482	8465	X-RAY DIFFRACTION	99.99
2.1-2.13	0.3203	140	0.3015	8439	X-RAY DIFFRACTION	100
2.13-2.16	0.3055	141	0.2848	8442	X-RAY DIFFRACTION	100
2.16-2.19	0.3041	143	0.2716	8418	X-RAY DIFFRACTION	100
2.19-2.23	0.3152	138	0.2639	8492	X-RAY DIFFRACTION	100
2.23-2.27	0.3137	141	0.2591	8441	X-RAY DIFFRACTION	100
2.27-2.31	0.2974	140	0.2542	8505	X-RAY DIFFRACTION	100
2.31-2.35	0.2926	143	0.254	8419	X-RAY DIFFRACTION	100
2.35-2.4	0.2766	140	0.2377	8441	X-RAY DIFFRACTION	99.99
2.4-2.45	0.2595	142	0.237	8437	X-RAY DIFFRACTION	100
2.45-2.51	0.3003	139	0.2228	8478	X-RAY DIFFRACTION	100
2.51-2.57	0.2315	145	0.2222	8417	X-RAY DIFFRACTION	100
2.57-2.64	0.2622	138	0.2128	8462	X-RAY DIFFRACTION	100
2.64-2.72	0.2366	141	0.2165	8443	X-RAY DIFFRACTION	100
2.72-2.81	0.2338	137	0.2086	8435	X-RAY DIFFRACTION	100
2.81-2.91	0.2317	142	0.2316	8500	X-RAY DIFFRACTION	100
2.91-3.03	0.293	136	0.214	8417	X-RAY DIFFRACTION	100
3.03-3.16	0.2892	143	0.2152	8448	X-RAY DIFFRACTION	100
3.16-3.33	0.2012	141	0.197	8456	X-RAY DIFFRACTION	100
3.33-3.54	0.229	146	0.2041	8453	X-RAY DIFFRACTION	100
3.54-3.81	0.1577	143	0.1614	8441	X-RAY DIFFRACTION	100
3.81-4.2	0.2003	141	0.1502	8442	X-RAY DIFFRACTION	99.99
4.2-4.8	0.1598	142	0.1446	8465	X-RAY DIFFRACTION	99.99
4.8-6.05	0.1746	140	0.1729	8442	X-RAY DIFFRACTION	100
6.05-45.33	0.1813	147	0.1599	8419	X-RAY DIFFRACTION	99.62

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	3.07239782015	0.157265667495	0.666450598384	4.04786270874	-0.632979249919	2.63259152199	0.0545927786836	-0.195239292228	-0.315143616927	-0.00710826806117	-0.0865802200913	-0.1185312343	0.254536423925	0.160767382729	0.0282756727749	0.31707607148	0.06684366617	0.0579604469558	0.356946175768	0.0452598456802	0.332809634655	150.711	20.957	88.577
2	4.31353617896	-0.40734191383	0.436732356789	1.59857345425	-0.341911726202	1.8154830669	-0.0880377149378	-0.63932839012	-0.12438187551	0.296575933728	0.0299497216869	-0.0761697743213	0.228399223551	-0.0757914972867	0.0462605882788	0.404883247294	0.0190894304895	-0.00994915027178	0.356639631896	0.111099471927	0.328686329962	139.374	18.411	99.782
3	2.14805852653	0.730307310577	0.11069943338	1.26027194513	0.0597413496442	0.615461602833	0.0499250258909	-0.445866447516	0.0982547815592	0.15714310767	-0.083730188471	-0.134520159486	-0.000625955649607	0.140676693514	0.0314350505053	0.328733982084	0.0304869132574	-0.0382616636794	0.485507572251	0.0080121752777	0.320693202916	151.68	37.688	101.076
4	7.06162110209	-5.07860945181	3.39109973498	4.68999817843	-3.67710160927	5.16491450934	0.056703587007	-0.239041535604	0.121480854389	-0.292745189533	0.0157890179737	0.129706520506	0.412531925408	-0.41274829996	-0.102815732557	0.287662035963	0.0201480139024	0.00622190813204	0.43480180938	-0.038660711766	0.418642852408	120.144	30.004	89.67
5	3.50347259988	0.482901804671	-0.591021542165	2.82626657482	0.128668207786	3.13126803574	-0.0753263349789	0.222830984194	-0.0289588139158	-0.283123346432	-0.0236526717977	0.199264135467	0.144746614937	-0.304951586442	0.105166383927	0.405240797312	0.00022063655483	-0.0886719276819	0.432387083774	0.0179084287149	0.338971564038	86.358	46.362	61.856
6	0.997275446187	-0.018903961784	0.0768269867619	2.93385503023	0.0615996661641	4.36230452642	-0.0756504027325	-0.0766624095661	-0.275892054364	-0.0307111014504	0.201489194565	-0.0263030542836	0.359762175542	0.129779921872	-0.112503839233	0.270740528989	0.010296319212	-0.0076810632234	0.460979696093	-0.0279578643889	0.435674718598	89.469	39.923	82.079
7	3.09239960943	-0.0393132865655	-0.637065239188	0.95031791684	-0.0191901250173	1.59357574085	-0.103360335775	0.31231469524	-0.46179328068	-0.337330902568	0.0050642252336	0.0385606557248	0.533893898913	-0.00856022362146	0.124393264492	0.645214960588	-0.0254687274464	-0.00792633983024	0.422248313207	-0.0850916560552	0.478319181537	100.266	31.332	60.806
8	2.4885437585	0.666667824162	-0.0482279067838	2.10810959629	0.219580159939	2.93422034683	-0.0958868955612	-0.215460161714	0.549910317157	0.148675535001	0.163883276183	-0.136765786492	-0.110538006844	0.181641445044	-0.0898479079517	0.287835778208	0.0450303820741	-0.0776404657064	0.476688120922	-0.0629611524685	0.417116640959	102.972	50.095	91.237
9	3.08395098074	-0.275752599566	-0.0994412691739	2.92951959708	1.05167694491	3.53872352774	-0.00812217889002	-0.186862898464	0.124870293676	0.39023660302	0.136319083421	-0.0505501053284	-0.0300623559866	0.138759433559	-0.105048172133	0.473969350793	-0.0236479604611	0.033177747026	0.4630842402	-0.0789344161959	0.290646216508	125.919	85.787	116.713
10	3.58075189844	-0.0960221699814	-0.60819467417	6.17000199439	1.19793961662	0.718263409636	0.0849081753299	-0.221945747609	-0.25269290167	0.51029093655	-0.262027894888	0.75680996671	0.0389665106497	-0.286694959646	0.185209141675	0.541055597659	-0.0158719245529	0.0839514573032	0.61474049137	-0.0485773087001	0.380897362934	115.999	66.912	119.664
11	1.88470609502	0.481411847592	0.364015938113	2.65561202256	-0.177816826442	2.06393912923	-0.0601116002743	-0.137329011895	0.344798116029	0.16393326746	0.130806157896	0.554653169064	-0.239113315086	-0.290084337589	-0.0756089224568	0.335198928765	0.0696924599449	0.0610965971121	0.488450622307	-0.0555789532081	0.488979946434	108.8	86.861	105.382
12	2.29498125585	-1.41394559218	-0.340447462629	4.37251782848	-1.15286656243	2.94846957901	0.104393878411	0.0252295744473	-0.412268216742	0.201003382257	-0.0366637584322	0.207878230541	0.083902846911	0.43311168049	-0.0305456362336	0.443985213012	-0.0251539391402	-0.0535155948893	0.5118788397	-0.121433678198	0.550200912751	122.151	53.355	107.695

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 3:90 )	A	3 - 90
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 91:243 )	A	91 - 243
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 244:388 )	A	244 - 388
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 389:441 )	A	389 - 441
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 3:114 )	B	3 - 114
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 115:227 )	B	115 - 227
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 228:362 )	B	228 - 362
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 363:441 )	B	363 - 441
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 2:114 )	C	2 - 114
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 115:227 )	C	115 - 227
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 228:362 )	C	228 - 362
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 363:441 )	C	363 - 441

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