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- PDB-3f6m: 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: 3f6m | ||||||
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Title | Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis Authors: Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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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: 17663.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal fusion of maltose-binding protein (removed in situ) and N-terminal His-tag which is removed during the purification Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8ZBP7, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0M Ammonium sulfate, 0.1M HEPES, pH 7.0, 0.5 %w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.95→46.37 Å / Num. all: 11110 / Num. obs: 11110 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 77.61 Å2 / Rmerge(I) obs: 0.131 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.7 / Num. unique all: 554 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 98.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→46.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→3.037 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 100.486 Å / Origin y: 82.277 Å / Origin z: 84.489 Å
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