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Yorodumi- PDB-3fpi: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fpi | ||||||
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Title | Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / CSGID / alpha-beta sandwich / Isoprene biosynthesis / Metal-binding / Structural Genomics / Structural Genomics of National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information 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 | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD/molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate Authors: Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fpi.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fpi.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fpi_validation.pdf.gz | 765.6 KB | Display | wwPDB validaton report |
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Full document | 3fpi_full_validation.pdf.gz | 771.2 KB | Display | |
Data in XML | 3fpi_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3fpi_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fpi ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fpi | HTTPS FTP |
-Related structure data
Related structure data | 3f6mS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17663.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal maltose binding protein fusion and 6-his tag with the TEV protease cut-site. The MBP fusion is removed in situ and the tag is removed during the purification Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ispF, y0829, YPO3360, YPTB0771, YP_0327 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: Q8ZBP7, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 6 types, 82 molecules
#2: Chemical | ChemComp-CTP / | ||
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#3: Chemical | ChemComp-EPE / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-SO4 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9786 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 2, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→34.33 Å / Num. all: 12751 / Num. obs: 12751 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 83.86 Å2 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 2.1 / Num. unique all: 620 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD/molecular replacement Starting model: 3F6M Resolution: 2.8→34.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 15.153 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.19 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: 68.782 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.805→2.877 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.0826 Å / Origin y: 8.7153 Å / Origin z: 11.2289 Å
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