+Open data
-Basic information
Entry | Database: PDB / ID: 6oiv | |||||||||
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Title | XFEL structure of Escherichia coli dGTPase | |||||||||
Components | Deoxyguanosinetriphosphate triphosphohydrolase | |||||||||
Keywords | metal 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 / manganese ion binding / single-stranded DNA binding / GTPase activity / magnesium ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.06 Å | |||||||||
Authors | Barnes, C.O. / Wu, Y. / Calero, G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oiv.cif.gz | 601.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oiv.ent.gz | 503.3 KB | Display | PDB format |
PDBx/mmJSON format | 6oiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oiv ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oiv | HTTPS FTP |
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-Related structure data
Related structure data | 6oi7SC 6oiwC 6oixC 6oiyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.5 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0 and 1.6 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.307 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Dec 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.307 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 measurement | Collection time total: 6 hours / Focal spot size: 3 µm2 / Pulse duration: 30 fsec. / Pulse photon energy: 9.5 keV |
Serial crystallography sample delivery | Description: Loop / Method: fixed target |
Serial crystallography sample delivery fixed target | Crystals per unit: 6 / Description: Grid / Sample holding: Grid / Sample unit size: 600 µm / Support base: Goniometer |
Serial crystallography data reduction | Crystal hits: 233 / Frame hits: 261 / Frames failed index: 22 / Frames indexed: 211 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 64.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.06→61.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.06→3.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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