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Yorodumi- PDB-3esj: Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3esj | ||||||
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Title | Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / MECDP-synthase / Isoprene biosynthesis / Magnesium / Manganese / Metal-binding | ||||||
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 / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Hunter, W.N. / Ramsden, N.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy Authors: Ramsden, N.L. / Buetow, L. / Dawson, A. / Kemp, L.A. / Ulaganathan, V. / Brenk, R. / Klebe, G. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3esj.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esj.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 3esj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esj_validation.pdf.gz | 983.5 KB | Display | wwPDB validaton report |
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Full document | 3esj_full_validation.pdf.gz | 988.8 KB | Display | |
Data in XML | 3esj_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3esj_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esj ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esj | HTTPS FTP |
-Related structure data
Related structure data | 3elcC 3eorC 3ernC 3fbaC 1gx1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 17576.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ispF / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CC7 / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GPP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.152275 Å3/Da / Density % sol: 82.802673 % / Mosaicity: 0.6 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M ammonium formate, HEPES, 5% butanediol, pH 7.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2003 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→29.495 Å / Num. obs: 13946 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 8.9 / Redundancy: 14.5 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 5.995 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GX1 Resolution: 2.7→24.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.854 / SU B: 6.281 / SU ML: 0.127 / SU R Cruickshank DPI: 0.212 / SU Rfree: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.13 Å2 / Biso mean: 40.065 Å2 / Biso min: 2.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→24.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.701→2.771 Å / Total num. of bins used: 20
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