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- PDB-6oix: Structure of Escherichia coli dGTPase bound to GTP -

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Basic information

Entry
Database: PDB / ID: 6oix
TitleStructure of Escherichia coli dGTPase bound to GTP
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase
Keywordsmetal binding protein / hydrolase / dNTP Triphosphohydrolase / Metalloenzyme / XFEL / E. coli dGTPase
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
GUANOSINE-5'-TRIPHOSPHATE / : / Deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBarnes, C.O. / Wu, Y. / Calero, G.
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 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)360,29418
Polymers356,8256
Non-polymers3,46912
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28600 Å2
ΔGint-92 kcal/mol
Surface area100430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.587, 191.587, 292.870
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: 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: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15723, dGTPase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / 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: SSRL / Beamline: BL12-2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.15→40 Å / Num. obs: 87450 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 93.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.337 / Rpim(I) all: 0.122 / Net I/σ(I): 7.5
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 3.02 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3646 / CC1/2: 0.401 / Rpim(I) all: 0.941 / % possible all: 54.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→31.75 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.347
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2607 3.02 %RANDOM
Rwork0.19 ---
obs0.191 86451 91.6 %-
Displacement parametersBiso mean: 123.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.5702 Å20 Å20 Å2
2--2.5702 Å20 Å2
3----5.1403 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 3.15→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23733 0 198 216 24147
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0124504HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1233152HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8730SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4172HARMONIC5
X-RAY DIFFRACTIONt_it24504HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion21.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3017SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28686SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3122 -2.49 %
Rwork0.2734 3646 -
all0.2744 3739 -
obs--54.46 %
Refinement TLS params.

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

IDL11 (°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)
12.77731.2488-1.01362.2311-1.37892.333-0.04540.0409-0.4354-0.0194-0.1678-0.31780.17310.29380.2132-0.26680.0366-0.0334-0.2170.02750.020858.139935.869625.8823
22.9498-0.28230.76551.7154-0.08574.38980.0888-0.4666-0.24120.1794-0.1358-0.31950.94660.53450.047-0.29880.1454-0.13610.01190.1997-0.062569.32667.980971.7684
34.9545-0.3658-0.9291.622-0.36031.36390.24680.0715-0.113-0.2362-0.1210.07870.1380.0245-0.1258-0.2717-0.03350.0186-0.22360.0910.001717.644316.392155.9154
42.9472-1.35870.26812.5009-0.60822.0918-0.0106-0.27160.30810.5267-0.1495-0.4928-0.11430.43080.1601-0.3445-0.2171-0.25030.2380.0282-0.124170.010438.685388.8756
53.92560.6699-0.63111.8625-0.46371.13170.0499-0.5010.08630.29630.0626-0.1023-0.2720.12-0.1125-0.2957-0.0690.0516-0.074-0.0611-0.02917.31145.138976.7067
61.88810.7348-0.72571.777-0.79433.39440.2212-0.37890.51670.1245-0.17720.3137-0.3269-0.2063-0.044-0.3443-0.090.0409-0.1505-0.07250.072456.185766.651943.5893
71.47820.5479-0.16540-0.62110.7455-0.0099-0.19140.0067-0.05880.08910.09160.21610.307-0.0792-0.0626-0.02410.0071-0.02940.02150.107848.082235.194460.5565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|504 }A3 - 504
2X-RAY DIFFRACTION2{ B|3 - B|504 }B3 - 504
3X-RAY DIFFRACTION3{ C|3 - C|504 }C3 - 504
4X-RAY DIFFRACTION4{ D|4 - D|504 }D4 - 504
5X-RAY DIFFRACTION5{ E|2 - E|504 }E2 - 504
6X-RAY DIFFRACTION6{ F|3 - F|503 }F3 - 503
7X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }A601
8X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }C601
9X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }B601
10X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }E601
11X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }D601
12X-RAY DIFFRACTION7{ A|601 - A|601 C|601 - C|601 B|601 - B|601 E|601 - E|601 D|601 - D|601 F|601 - F|601 }F601

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