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- PDB-6oi7: Se-Met structure of apo- Escherichia coli dGTPase -

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Basic information

Entry
Database: PDB / ID: 6oi7
TitleSe-Met structure of apo- Escherichia coli dGTPase
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase
KeywordsMETAL BINDING PROTEIN / E.coli dGTPase / Metalloenzymes / dNTP Triphosphohydrolase
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
Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsCalero, G. / Barnes, C.O. / Wu, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112686 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM116642 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.
Authors: Barnes, C.O. / Wu, Y. / Song, J. / Lin, G. / Baxter, E.L. / Brewster, A.S. / Nagarajan, V. / Holmes, A. / Soltis, S.M. / Sauter, N.K. / Ahn, J. / Cohen, A.E. / Calero, G.
History
DepositionApr 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyguanosinetriphosphate triphosphohydrolase
B: Deoxyguanosinetriphosphate triphosphohydrolase
C: Deoxyguanosinetriphosphate triphosphohydrolase
D: Deoxyguanosinetriphosphate triphosphohydrolase
E: Deoxyguanosinetriphosphate triphosphohydrolase
F: Deoxyguanosinetriphosphate triphosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,11421
Polymers359,9206
Non-polymers1,19415
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25960 Å2
ΔGint-211 kcal/mol
Surface area109310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.183, 192.183, 287.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Deoxyguanosinetriphosphate triphosphohydrolase / dGTPase


Mass: 59986.715 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 / Variant: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: P15723, dGTPase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.0 and 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 124944 / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.277 / Net I/σ(I): 15.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 15.5 % / Rmerge(I) obs: 3.08 / Mean I/σ(I) obs: 1 / Num. unique obs: 4448 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.1_3469: ???)refinement
TRUNCATEdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.97 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3557 3 %Random
Rwork0.185 ---
obs0.187 118509 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24759 0 51 13 24823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125371
X-RAY DIFFRACTIONf_angle_d1.24334311
X-RAY DIFFRACTIONf_dihedral_angle_d15.16215259
X-RAY DIFFRACTIONf_chiral_restr0.0623649
X-RAY DIFFRACTIONf_plane_restr0.0084407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9036-2.94340.34751400.32324448X-RAY DIFFRACTION99
2.9434-2.98540.35721410.30634558X-RAY DIFFRACTION100
2.9854-3.030.38451440.30934529X-RAY DIFFRACTION100
3.03-3.07730.31721250.28944543X-RAY DIFFRACTION100
3.0773-3.12780.34131380.28514552X-RAY DIFFRACTION100
3.1278-3.18170.35321460.27464548X-RAY DIFFRACTION100
3.1817-3.23950.34491440.26044543X-RAY DIFFRACTION100
3.2395-3.30180.29531350.23694552X-RAY DIFFRACTION100
3.3018-3.36920.27531260.22794583X-RAY DIFFRACTION100
3.3692-3.44250.29161330.22094576X-RAY DIFFRACTION100
3.4425-3.52250.28951240.20984571X-RAY DIFFRACTION100
3.5225-3.61060.26531450.20594563X-RAY DIFFRACTION100
3.6106-3.70820.26211530.20034564X-RAY DIFFRACTION100
3.7082-3.81730.23411350.18034557X-RAY DIFFRACTION100
3.8173-3.94040.2491290.17484610X-RAY DIFFRACTION100
3.9404-4.08120.24161470.17114583X-RAY DIFFRACTION100
4.0812-4.24450.19851480.15454591X-RAY DIFFRACTION100
4.2445-4.43760.20371450.14684592X-RAY DIFFRACTION100
4.4376-4.67140.15941380.14214618X-RAY DIFFRACTION100
4.6714-4.96380.21881700.14354583X-RAY DIFFRACTION100
4.9638-5.34670.20421390.15784651X-RAY DIFFRACTION100
5.3467-5.8840.20481390.18374658X-RAY DIFFRACTION100
5.884-6.73360.2641400.20934689X-RAY DIFFRACTION100
6.7336-8.4770.24831680.1814732X-RAY DIFFRACTION100
8.477-49.97780.19351650.16684958X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4463-0.2962-0.53472.3315-0.83082.6297-0.06180.76760.4023-0.12050.31620.083-0.694-0.0336-0.20150.6312-0.0025-0.07740.70820.10840.58253.900751.964310.5296
21.44020.0939-1.26331.5053-0.78912.6639-0.0394-0.5657-0.22550.2041-0.2308-0.03270.27850.60580.23430.7265-0.03750.00750.80970.17210.769963.367547.927831.7129
31.78780.673-1.65611.06490.16381.8710.00030.5187-0.2881-0.0935-0.2393-0.0119-0.36930.17910.21680.4527-0.0203-0.14330.86670.14240.644463.209949.125218.127
42.18390.34930.08716.51373.8895.0898-0.16050.101-1.11130.13450.287-0.42961.60360.4076-0.18681.08720.17180.05060.7028-0.00471.212354.454814.37127.0422
52.86691.1524-0.5373.2983-1.4512.2708-0.280.3001-0.6087-0.34320.144-0.28260.56410.0610.05940.7544-0.0030.00730.6638-0.08580.613455.771128.579516.1706
62.26920.63681.87390.6428-0.13355.21710.4735-0.2506-0.84470.21880.1048-0.47470.00421.5839-0.61920.7680.0194-0.05191.29560.17890.910980.480444.007237.2057
71.1240.82670.53180.9914-1.09113.6390.0871-0.3927-0.20480.1282-0.2179-0.31430.1330.44610.16070.68960.0936-0.01520.99560.12580.879377.718643.084427.3325
87.18761.74771.93394.03171.50955.39170.0123-1.0838-0.60730.20330.4351-0.4731-0.66980.1939-0.46140.57230.07410.0310.53420.10250.470653.755624.776741.2205
91.78360.34040.02992.5018-1.34322.1084-0.24780.1972-0.3696-0.21850.51190.12370.457-0.9378-0.19950.8021-0.18580.00310.85340.14130.696134.098324.844726.8186
102.85670.8494-0.02283.8034-0.59721.77470.0504-0.4175-0.12780.6839-0.33610.2345-0.0964-0.07250.24010.6199-0.07210.03720.62880.04260.697945.497527.735434.5092
111.0803-1.4056-0.30172.4294-1.2691.38160.0207-0.87760.0850.6852-0.0508-0.5790.45670.293-0.03531.1540.0344-0.32351.67740.14981.089977.506413.768781.3397
123.3982-1.08581.03172.2626-0.13141.98310.1363-0.3455-0.51480.131-0.2516-0.33690.84690.21260.08381.09430.1822-0.0981.07250.07770.908471.44691.768667.4047
131.0233-0.3896-0.27382.1736-0.49731.4624-0.0021-0.4604-0.20271.12810.2616-0.05271.0048-0.2712-0.20121.584-0.1329-0.29291.3260.13830.840261.27235.661587.8673
141.90040.18030.48482.9154-0.52413.608-0.01690.22170.3935-0.0278-0.1746-0.31210.25640.30340.19450.7590.1213-0.09410.96050.10190.655767.66714.397851.9038
151.6628-0.49751.26211.65930.24592.68270.0398-0.20380.02260.11820.03540.06420.01610.1274-0.07370.55080.04880.13930.73880.11860.79148.831421.771264.1741
162.6758-0.26461.44741.63321.01611.59870.2089-0.4086-0.2467-0.10820.07410.18650.4901-0.1711-0.31260.5652-0.06040.00950.59990.26790.77893.646120.445361.1224
172.8568-0.4512-0.69721.8388-0.11331.28390.08430.2515-0.4886-0.5516-0.1001-0.11760.17050.1848-0.05890.75650.03130.01670.685-0.03490.766324.31433.458750.1344
181.8286-0.6007-0.32611.55030.69250.55140.12260.4102-0.364-0.07220.1039-0.16210.1907-0.0679-0.20980.7496-0.0446-0.02880.66580.03130.736310.519114.032651.0795
196.733-1.79310.1025.6286-0.74722.39180.41461.43751.2343-1.0975-0.34230.5777-0.10150.1799-0.06960.8215-0.0811-0.00620.88050.32731.01310.940644.331139.5866
204.47160.6874-0.85583.0275-1.15792.1740.00390.48710.5725-0.56890.27690.59270.01160.0759-0.2790.64120.003-0.00430.78530.10520.69475.857429.643745.5133
212.0194-1.33720.50965.5118-1.62542.3044-0.026-0.4081-0.3955-0.30370.0428-0.16160.28780.40440.0690.4210.11990.07080.83190.19170.745539.32149.284157.2725
222.3569-1.47460.11662.65370.03293.02860.151-0.5658-0.1769-0.2336-0.1619-0.09120.14620.23490.00830.70130.07180.02840.77950.06760.827134.08757.297361.6076
231.8975-0.38630.47830.5951-0.31640.80090.39470.28410.94680.3028-0.4349-0.73130.96450.4070.13222.3227-0.0117-1.49551.38850.02560.204574.187123.4629104.1779
241.692-0.9337-0.34412.49220.35312.8048-0.76410.46730.87270.05520.3271-0.89050.0830.11530.23681.0636-0.084-0.44861.13660.19091.243474.823828.332281.1967
251.6662-0.13480.56470.48750.410.45340.2599-1.02740.29780.8107-0.3275-0.30940.4551-0.34520.07391.4289-0.1822-0.45781.3580.12531.095579.701127.895394.2102
261.2312-1.9674-0.80624.2245-0.90826.562-0.24580.01960.48551.07260.2198-0.9168-0.2693-0.3822-0.18481.21-0.1889-0.2251.2554-0.09241.094159.177258.928989.708
271.7992-0.9521-1.02673.0732-0.07491.44610.0681-0.46580.49071.40620.0008-1.11890.04210.3896-0.15721.3619-0.1917-0.3781.3593-0.30621.132568.581345.967498.5951
282.48130.01220.622.28970.26182.77250.71370.03660.04070.3035-0.3957-1.39020.07370.5713-0.28380.7818-0.1532-0.16171.52770.05111.531381.975536.080671.2014
291.563-0.75761.00120.4585-0.63091.0184-0.06941.03720.2998-1.0947-0.7522-0.3434-0.58310.44330.18921.15810.0535-0.20591.89350.14621.984696.090135.109966.319
300.8202-0.97491.02761.2736-0.88213.0044-0.0363-0.09530.84880.4604-0.0091-1.24690.15130.25540.03560.8807-0.119-0.46861.58930.05541.799187.974936.680680.4775
315.0819-0.818-3.72762.32260.75155.62330.70170.80280.8069-0.15180.4408-0.58050.05130.239-0.85450.6218-0.1399-0.17310.9862-0.10480.790556.729947.643376.1943
321.6963-0.39470.40152.3206-0.72343.41590.0352-1.04540.271.09970.18940.1530.1968-0.052-0.24471.1824-0.08830.00761.4502-0.16070.722543.74243.500196.2117
332.7763-1.3528-0.74822.456-0.36451.26730.2309-0.07340.19720.1806-0.24710.13790.2013-0.4018-0.14850.8286-0.1274-0.03841.1924-0.1160.692152.260343.209785.1345
341.6106-0.7788-0.82412.125-0.23012.9637-0.0321-0.0211-0.28740.09320.09110.01110.0266-0.1426-0.02440.5007-0.08240.07510.64850.03090.8067.644337.017869.7448
351.49860.6404-0.21041.74070.15880.75830.1276-0.43430.20080.31370.143-0.3226-0.32310.0891-0.2070.7202-0.03020.07740.8426-0.07390.90516.66754.053977.5712
362.0548-0.2917-0.23832.6158-0.56121.2088-0.1168-0.6356-0.13970.50120.0385-0.0759-0.00380.36460.07970.6668-0.0224-0.00470.95780.01310.586815.099332.553586.3763
371.7946-0.3462-0.39681.9085-0.46832.26480.23760.21840.2742-0.1176-0.093-0.0521-0.30650.3773-0.09090.565-0.1610.1250.8021-0.01231.071529.961458.059265.278
381.34650.28360.78612.3993-1.15971.1633-0.1298-0.01640.2232-0.1365-0.0233-0.09030.0836-0.09190.17740.6528-0.02660.01560.67780.04630.745862.431562.344831.7175
391.39610.3857-0.39371.773-0.08871.47410.1908-0.24910.52430.2123-0.17940.2824-0.1734-0.16770.00360.6499-0.04990.06250.7384-0.03960.800952.881570.111242.3069
402.47581.28450.52840.1884-0.73452.28490.21-0.09810.28690.15550.150.5021-0.1402-0.6088-0.17690.60550.12650.09450.6019-0.03210.949344.690564.920437.6551
413.2595-0.1142-0.11831.45980.34613.20890.3687-0.8216-0.35220.456-0.3444-0.3178-0.09530.15290.02760.7395-0.24510.01880.9809-0.00570.560667.033261.29963.1631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 40 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 90 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 91 THROUGH 125 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 126 THROUGH 157 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 158 THROUGH 258 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 259 THROUGH 327 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 328 THROUGH 393 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 394 THROUGH 418 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 419 THROUGH 468 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 469 THROUGH 504 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 3 THROUGH 90 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 91 THROUGH 236 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 237 THROUGH 393 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 394 THROUGH 504 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 3 THROUGH 90 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 91 THROUGH 124 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 125 THROUGH 219 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 220 THROUGH 282 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 283 THROUGH 328 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 329 THROUGH 393 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 394 THROUGH 437 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 438 THROUGH 504 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 3 THROUGH 40 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 41 THROUGH 90 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 91 THROUGH 124 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 125 THROUGH 160 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 161 THROUGH 260 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 261 THROUGH 296 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 297 THROUGH 328 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 329 THROUGH 393 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 394 THROUGH 418 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 419 THROUGH 468 )
33X-RAY DIFFRACTION33CHAIN 'D' AND (RESID 469 THROUGH 504 )
34X-RAY DIFFRACTION34CHAIN 'E' AND (RESID 3 THROUGH 90 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 91 THROUGH 219 )
36X-RAY DIFFRACTION36CHAIN 'E' AND (RESID 220 THROUGH 393 )
37X-RAY DIFFRACTION37CHAIN 'E' AND (RESID 394 THROUGH 504 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 3 THROUGH 90 )
39X-RAY DIFFRACTION39CHAIN 'F' AND (RESID 91 THROUGH 327 )
40X-RAY DIFFRACTION40CHAIN 'F' AND (RESID 328 THROUGH 418 )
41X-RAY DIFFRACTION41CHAIN 'F' AND (RESID 419 THROUGH 504 )

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