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- PDB-8fvc: E coli. CTP synthase in complex with dF-dCTP (potassium malonate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fvc | |||||||||
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Title | E coli. CTP synthase in complex with dF-dCTP (potassium malonate + 5 mM MgCl2) | |||||||||
![]() | CTP synthase | |||||||||
![]() | CYTOSOLIC PROTEIN / LIGASE / Inhibitor complex / Metabolic enzyme | |||||||||
Function / homology | ![]() CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / glutamine metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Holyoak, T. / McLeod, M.J. / Tran, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate. Authors: McLeod, M.J. / Tran, N. / McCluskey, G.D. / Gillis, T.D. / Bearne, S.L. / Holyoak, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fv6C ![]() 8fv7C ![]() 8fv8C ![]() 8fv9C ![]() 8fvaC ![]() 8fvbC ![]() 8fvdC ![]() 8fveC ![]() 8sbrC ![]() 5tkvS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60446.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B7MLA1, CTP synthase (glutamine hydrolysing) #2: Chemical | ChemComp-MLA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.54 Å3/Da / Density % sol: 72.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3777 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→81.7 Å / Num. obs: 103987 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 0.994 / CC star: 1 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.041 / Rrim(I) all: 0.147 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 7.11 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 10148 / CC1/2: 0.629 / CC star: 0.92 / Rpim(I) all: 0.458 / Rrim(I) all: 1.243 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TKV Resolution: 2.281→81.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.083 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.153 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 | Biso mean: 45.715 Å2
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Refinement step | Cycle: LAST / Resolution: 2.281→81.7 Å
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Refine LS restraints |
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LS refinement shell |
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