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- PDB-5iwx: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iwx | ||||||
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Title | Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Z.C. / Jin, Y. / Wang, G.G. | ||||||
![]() | ![]() Title: Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway. Authors: Liu, Z.C. / Jin, Y. / Liu, W.F. / Tao, Y. / Wang, G.G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.3 KB | Display | ![]() |
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PDB format | ![]() | 150.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.5 KB | Display | ![]() |
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Full document | ![]() | 475.7 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 49.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iwyC ![]() 1t0aS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17147.693 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ispF, yacN, BSU00910 / Production host: ![]() ![]() References: UniProt: Q06756, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25mM Tris-HCl PH 8.0, 0.1M NaCl, 0.1M Magnesium formate dihydrate, 12-15% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. obs: 56504 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T0A Resolution: 1.99→29.054 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.838 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.173 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→29.054 Å
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Refine LS restraints |
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