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- PDB-6oiv: XFEL structure of Escherichia coli dGTPase -

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Basic information

Entry
Database: PDB / ID: 6oiv
TitleXFEL structure of Escherichia coli dGTPase
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
: / Deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.06 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 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25210 Å2
ΔGint-201 kcal/mol
Surface area110040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.589, 192.589, 291.254
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 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 8 / 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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 279 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: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.307 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.307 Å / Relative weight: 1
ReflectionResolution: 3.06→25 Å / Num. obs: 103325 / % possible obs: 97.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 2.46 Å2 / CC1/2: 0.32 / R split: 0.39 / Rmerge(I) obs: 0.66 / Net I/σ(I): 6.1
Reflection shellResolution: 3.06→3.12 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4041 / CC1/2: 0.23 / R split: 0.88 / Rrim(I) all: 0.84 / % possible all: 91.4
Serial crystallography measurementCollection time total: 6 hours / Focal spot size: 3 µm2 / Pulse duration: 30 fsec. / Pulse photon energy: 9.5 keV
Serial crystallography sample deliveryDescription: Loop / Method: fixed target
Serial crystallography sample delivery fixed targetCrystals per unit: 6 / Description: Grid / Sample holding: Grid / Sample unit size: 600 µm / Support base: Goniometer
Serial crystallography data reductionCrystal hits: 233 / Frame hits: 261 / Frames failed index: 22 / Frames indexed: 211

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OI7

6oi7


Resolution: 3.06→61.2 Å / Cor.coef. Fo:Fc: 0.742 / Cor.coef. Fo:Fc free: 0.691 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2922 3.06 %RANDOM
Rwork0.225 ---
obs0.226 95415 92.3 %-
Displacement parametersBiso mean: 64.33 Å2
Baniso -1Baniso -2Baniso -3
1-5.1391 Å20 Å20 Å2
2--5.1391 Å20 Å2
3----10.2782 Å2
Refine analyzeLuzzati coordinate error obs: 0.65 Å
Refinement stepCycle: 1 / Resolution: 3.06→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24723 0 51 8 24782
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125369HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1534307HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9048SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes613HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3671HARMONIC5
X-RAY DIFFRACTIONt_it25369HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion22.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3111SEMIHARMONIC5
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_contact31331SEMIHARMONIC4
LS refinement shellResolution: 3.06→3.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 161 3.29 %
Rwork0.281 4740 -
all0.282 4901 -
obs--65.18 %

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