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Yorodumi- PDB-3f6m: Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -
+Open data
-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 | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / alpha-beta structure / structural genomics of infectious diseases / Isoprene biosynthesis / Metal-binding / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
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 / Resolution: 2.96 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 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f6m.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f6m.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f6m_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 3f6m_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 3f6m_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3f6m_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6m ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6m | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-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.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ispF, y0829, YPO3360, YP_0327 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q8ZBP7, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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#2: 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-ID / Wavelength: 0.9793 Å |
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: 0.9793 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.96→46.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.21 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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