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- PDB-7qrh: Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qrh | ||||||
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Title | Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii. | ||||||
![]() | Aspartate/glutamate/uridylate kinase | ||||||
![]() | TRANSFERASE / Phosphate Kinase | ||||||
Function / homology | MfnE family / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / kinase activity / phosphorylation / Aspartate/glutamate/uridylate kinase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maddock, R.M.A. / Race, P.R. / Burton, N.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the 5-(aminomethyl)furan-3-yl methyl phosphate kinase MfnE from Methanococcus vannielii. Authors: Maddock, R.M.A. / Race, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25223.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % / Description: Teardrop hexagon. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.5, 35% w/v PAA 2100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→78.04 Å / Num. obs: 22089 / % possible obs: 100 % / Redundancy: 113.8 % / CC1/2: 1 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.36→2.45 Å / Num. unique obs: 2259 / CC1/2: 0.306 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TrRosetta Resolution: 2.36→74.717 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: FREE R-VALUE / ESU R: 0.318 / ESU R Free: 0.245 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.36→74.717 Å
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Refine LS restraints |
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LS refinement shell |
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