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- PDB-5hs2: Crystal structure of IspD complexed with CTP and Mg2+ from Bacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hs2 | ||||||
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Title | Crystal structure of IspD complexed with CTP and Mg2+ from Bacillus subtilis at 1.90 Angstroms resolution | ||||||
![]() | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Y. / Liu, Z.C. / Wang, G.G. | ||||||
![]() | ![]() Title: A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis. Authors: Jin, Y. / Liu, Z. / Li, Y. / Liu, W. / Tao, Y. / Wang, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.2 KB | Display | ![]() |
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Full document | ![]() | 835 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ddtC ![]() 5ddvC ![]() 2yc3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 25879.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ispD, yacM, BSU00900 / Production host: ![]() ![]() References: UniProt: Q06755, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase #2: Chemical | ChemComp-CTP / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES, 25% Polyethylene glycol 3350, 10mM CTP, 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.6 Å / Num. obs: 37021 / % possible obs: 98.8 % / Redundancy: 2.8 % / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YC3 Resolution: 1.9→29.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.126 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.755 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.6 Å
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Refine LS restraints |
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