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Yorodumi- PDB-3gf0: Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gf0 | |||||||||
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Title | Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q from Methanocaldococcus jannaschii in complex with pyrophosphate and magnesium | |||||||||
Components | dCTP deaminase, dUMP-forming | |||||||||
Keywords | HYDROLASE / dCTP deaminase-dUTPase / bifunctional hydrolase / magnesium / nucleotide metabolism | |||||||||
Function / homology | Function and homology information dCTP deaminase (dUMP-forming) / dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å | |||||||||
Authors | Siggaard, J.H.B. / Johansson, E. / Vognsen, T. / Helt, S.S. / Harris, P. / Willemoes, M. | |||||||||
Citation | Journal: To be Published Title: Pre-steady State Kinetic and Structural Evidence for a Concerted Biofunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii Authors: Siggaard, J.H.B. / Johansson, E. / Vognsen, T. / Helt, S.S. / Harris, P. / Larsen, S. / Willemoes, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gf0.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gf0.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gf0_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 3gf0_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 3gf0_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3gf0_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/3gf0 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/3gf0 | HTTPS FTP |
-Related structure data
Related structure data | 2hxbS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23460.869 Da / Num. of mol.: 1 / Mutation: E145Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q57872, dCTP deaminase (dUMP-forming) | ||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-POP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 20% PEG3350, 0.2M TRIPOTASSIUM CITRATE , pH 8.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→25 Å / Num. obs: 14787 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.101 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.62→2.69 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.434 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2HXB Resolution: 2.62→24.26 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.133 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.284 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.679 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→24.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.619→2.687 Å / Total num. of bins used: 20
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