PDB-7tu3: Structure of the L. blandensis dGTPase del55-58 mutant

ID or keywords:

Entry

Database: PDB / ID: 7tu3

Title

Structure of the L. blandensis dGTPase del55-58 mutant

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: 2.17 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	7tu3.cif.gz	548.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7tu3.ent.gz	432.6 KB	Display	PDB format
PDBx/mmJSON format	7tu3.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/7tu3 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tu3	HTTPS FTP

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Related structure data

Related structure data	26126C 26127C 26128C 26129C 7tu0C 7tu1C 7tu2C 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

158 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
315 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	181.410, 181.410, 110.858
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: 52296.719 Da / Num. of mol.: 3 / Mutation: del55-58 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.71 % Description: crystal grew as square bipyramid, approximately 400 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 (0.6M Sodium Potassium Tartrate, 0.2M 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 (0.6M Sodium Potassium Tartrate, 0.2M Lithium Sulfate, 0.1M Bis-Tris pH 6.5) and 10mg/mL protein. Cryoprotected by soaking in well solution with 30% ethylene glycol added

Crystal

Density Matthews: 3.05 Å³/Da / Density % sol: 59.71 %
Description: crystal grew as square bipyramid, approximately 400 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 (0.6M Sodium Potassium Tartrate, 0.2M 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: Nov 1, 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: 2.17→40 Å / Num. obs: 97009 / % possible obs: 99.2 % / Redundancy: 14.8 % / B_iso Wilson estimate: 55.76 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.154 / R_rim(I) all: 0.16 / Net I/σ(I): 8.88
Reflection shell	Resolution: 2.17→2.3 Å / Redundancy: 14.1 % / R_merge(I) obs: 1.243 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 14855 / CC_1/2: 0.745 / CC star: 0.924 / R_rim(I) all: 1.289 / % possible all: 95.4

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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: 2.17→39.89 Å / SU ML: 0.2891 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2223	3047	1.65 %
R_work	0.1939	181979	-
obs	0.1944	96798	98.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 67.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→39.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10165	0	50	180	10395

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0088	10388
X-RAY DIFFRACTION	f_angle_d	0.9989	14017
X-RAY DIFFRACTION	f_chiral_restr	0.0563	1549
X-RAY DIFFRACTION	f_plane_restr	0.0066	1814
X-RAY DIFFRACTION	f_dihedral_angle_d	16.134	3820

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 (%)
2.17-2.2	0.3645	115	0.3448	6497	X-RAY DIFFRACTION	77.91
2.2-2.24	0.3348	135	0.3092	8313	X-RAY DIFFRACTION	99.14
2.24-2.28	0.31	137	0.2898	8342	X-RAY DIFFRACTION	100
2.28-2.32	0.3055	140	0.2754	8345	X-RAY DIFFRACTION	100
2.32-2.36	0.2942	145	0.2708	8391	X-RAY DIFFRACTION	99.98
2.36-2.41	0.2459	140	0.2584	8362	X-RAY DIFFRACTION	99.96
2.41-2.46	0.2827	139	0.247	8354	X-RAY DIFFRACTION	100
2.46-2.52	0.2722	136	0.2274	8379	X-RAY DIFFRACTION	99.99
2.52-2.58	0.2375	145	0.2318	8360	X-RAY DIFFRACTION	100
2.58-2.65	0.2739	133	0.2135	8369	X-RAY DIFFRACTION	100
2.65-2.73	0.2403	141	0.223	8364	X-RAY DIFFRACTION	99.98
2.73-2.82	0.2276	140	0.2152	8405	X-RAY DIFFRACTION	100
2.82-2.92	0.31	136	0.2406	8357	X-RAY DIFFRACTION	100
2.92-3.04	0.2628	137	0.221	8349	X-RAY DIFFRACTION	100
3.04-3.18	0.2481	138	0.2262	8314	X-RAY DIFFRACTION	99.14
3.18-3.34	0.2306	140	0.2101	8318	X-RAY DIFFRACTION	100
3.34-3.55	0.2373	139	0.2163	8379	X-RAY DIFFRACTION	100
3.55-3.83	0.1637	148	0.1737	8381	X-RAY DIFFRACTION	100
3.83-4.21	0.2459	137	0.1653	8357	X-RAY DIFFRACTION	100
4.21-4.82	0.1936	141	0.1603	8382	X-RAY DIFFRACTION	100
4.82-6.07	0.2008	140	0.1798	8349	X-RAY DIFFRACTION	99.76
6.07-39.89	0.1879	145	0.1564	8312	X-RAY DIFFRACTION	99.44

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	4.47418888693	-0.448680695847	1.17672230557	4.59424918374	-0.689876734999	3.63539653025	0.0395524301951	-0.161431870276	-0.365821671924	-0.0383067615377	-0.0847793837013	-0.263275048534	0.362960013962	0.212826796225	0.0270465719808	0.364699818936	0.0953888073778	0.0426455209509	0.36621189296	0.0743489592147	0.388335920455	152.71	19.633	89.236
2	4.28312541349	-0.950483532988	-0.660124226606	3.16114430039	0.472516662607	3.65753746559	0.033053167835	-0.667510880324	-0.00941842524055	0.41393948174	-0.0248766549325	0.0412396428009	0.2975645357	0.00197115854658	0.00119796187354	0.493363443715	-0.0269072821217	0.042472406003	0.471808876258	0.080729703647	0.39966935588	134.565	21.013	101.013
3	1.89672687951	1.51304377998	-0.016677525293	3.74114036615	-0.0944207026442	0.518114545731	0.0918969110772	-0.350926838752	0.0355916209342	0.285476809908	-0.0552269246965	-0.041266971925	0.109271778078	0.14885316743	-0.0455763005395	0.400558861994	0.0545485520153	-0.0433761383806	0.578737554555	0.0560751388704	0.407322222122	156.708	35.874	100.478
4	2.63323456552	0.226138782598	0.230425549215	2.3197972717	-0.110037687499	0.900689250449	0.167777746001	-0.545880917903	0.200226421725	0.386104079798	-0.170073671029	0.0763428658186	0.056906120916	0.180188722568	-5.72439156355E-5	0.470714892025	0.0149479811199	0.0627388092242	0.565710078053	-0.00512337453163	0.318367692303	142.223	34.673	104.456
5	6.54200657741	-4.64026949876	3.50498870218	3.32355698174	-2.38119507045	4.32671701477	0.121316649226	-0.176930907012	0.573651461113	-0.362280168735	-0.135736602349	0.162934015113	0.177729613726	-0.105121969113	0.0424650839252	0.377471038036	0.0370018648275	0.0152876458722	0.417780281708	0.0178098026754	0.641166941649	120.452	30.469	89.865
6	5.08554169299	2.62379289384	-0.0261667709763	4.16769901807	0.544694879252	4.26281155838	-0.0440832848062	0.309029460284	0.269634481935	-0.127090532189	0.00575990532122	0.292825142923	-0.140152621731	-0.0902146747403	-0.0041728499293	0.477210014881	0.048811412621	-0.0796942625618	0.571685397575	0.00391185600567	0.421716017348	86.846	50.299	66.314
7	1.12614675178	0.184858260522	-0.263134219594	1.43583599011	-0.302931887907	3.52925821137	-0.0832070914718	0.161929700266	-0.190160564474	-0.283303137381	0.0804552707285	0.236065781788	0.338018169358	-0.120265469252	0.0113284134631	0.379032980624	-0.0208778775142	-0.0342225217428	0.493225390006	-0.0163095456839	0.504466071073	88.353	40.503	74.681
8	1.48171499649	0.0447905022438	-0.465217800113	0.921419958396	0.10689246075	2.03387278443	-0.0983778201997	0.257245413302	-0.330052255617	-0.346636394611	0.055789511745	-0.0726963373395	0.506129576824	0.108904907348	0.0385889107433	0.644829726021	-0.00177333325147	0.0232302444622	0.502066977763	-0.0613905289424	0.574228130238	101.52	33.447	65.405
9	5.47196809174	4.31344535964	3.89795209523	5.2293725489	2.53401583016	3.12693632403	0.083018819943	0.274463115153	0.506460438076	0.0839843523387	-0.0321916096287	0.173866224054	-0.0991869340618	0.284187545126	-0.029042820471	0.331114588173	0.0531709816579	0.00785216968113	0.49832523098	0.0270325312328	0.437363863722	101.383	53.167	92.498
10	2.70573275201	-1.00547442718	-0.745610574778	3.82975583194	1.50571150195	4.04921097835	-0.0479203781619	-0.37648458482	0.184213618259	0.410827142122	0.155603590376	-0.11326663711	-0.0287432083085	0.136872785905	-0.0415798498486	0.583378283484	-0.0247248678586	0.014028443312	0.544696502438	-0.10449157983	0.370896985328	125.864	86.071	117.184
11	2.17312615354	0.902522265429	-0.124998449377	5.262753713	1.1273543575	1.14310100812	-0.0557268941016	-0.524117587659	0.0227756741602	0.627416599909	0.00404274957677	0.401283841077	-0.144137070527	-0.211018156257	0.0501872897946	0.647962933607	0.0161247211295	0.134639539706	0.709697210584	-0.00429351483214	0.414076338305	115.773	67.094	119.995
12	1.48734553858	0.00673547245519	0.134833988801	3.11813952894	-1.62808000948	6.40566953091	0.00335441378485	-0.170382313067	0.312536087176	0.0724484088074	0.0990000692516	0.496224972326	0.0367981022735	-0.00343589595089	-0.133708053554	0.368499996821	0.0482727348973	0.0576888706741	0.453283266727	-0.0573635225235	0.503168596453	110.737	87.815	103.762
13	1.30281037325	-0.792827596655	-0.0699900468849	4.46795572972	0.149360484737	2.07093217467	0.0134361389983	-0.12611981608	0.125668628409	0.0829246600678	0.0511988230505	0.685794986826	-0.136241223369	-0.325583847734	-0.078176776664	0.351417952253	-0.0223260938303	0.0784668849105	0.646707340642	-0.0147116283397	0.503306514246	108.523	73.004	106.925
14	5.4366499115	-3.12280494916	-4.494342955	7.38726384549	5.62921162849	7.92363680737	0.18055302435	-0.751913485049	-0.737560772447	1.57150678312	-0.21478085481	-0.497707945232	0.442098306233	0.53563071694	-0.156998915384	0.772814090122	0.0342965595172	0.00412633396548	0.69203760539	0.0573821329781	0.541092108884	128.638	45.941	112.835
15	4.5639595518	-1.27097354394	-2.52252896517	7.86226036002	3.87114937394	7.95370376441	0.14128354667	-0.194026782769	-0.0962136277145	-0.253956386861	0.0345565289311	0.0604951675321	-0.814851745637	1.05564105055	-0.128971669396	0.553708970836	0.0102908837031	0.00950825705454	0.60572102943	0.00665174305279	0.432830227251	123.254	56.455	107.971

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 3:110 )	A	3 - 110
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 111:223 )	A	111 - 223
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 224:320 )	A	224 - 320
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 321:384 )	A	321 - 384
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 385:437 )	A	385 - 437
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 2:60 )	B	2 - 60
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 61:223 )	B	61 - 223
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 224:384 )	B	224 - 384
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 385:438 )	B	385 - 438
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 2:110 )	C	2 - 110
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 111:223 )	C	111 - 223
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 224:320 )	C	224 - 320
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 321:384 )	C	321 - 384
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 385:407 )	C	385 - 407
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 408:437 )	C	408 - 437

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