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Yorodumi- PDB-1i52: CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i52 | ||||||
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Title | CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS | ||||||
Components | 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE | ||||||
Keywords | TRANSFERASE / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESYS / MEP | ||||||
Function / homology | Function and homology information 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, M. / Cane, D.E. / Noel, J.P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. Authors: Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A.M. / Cane, D.E. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i52.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i52.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 1i52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i52 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i52 | HTTPS FTP |
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-Related 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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Details | The second monomer of the biological assembly (dimer) is generated by the two fold axis: -X,Y,-Z |
-Components
#1: Protein | Mass: 25772.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ISPD / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q46893, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CTP / |
#5: 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: 2.27 Å3/Da / Density % sol: 45.71 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 315.8 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, calcium acetate, magnesium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 42.8K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 2000 / Details: mirrors |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→90 Å / Num. all: 68287 / Num. obs: 68287 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 3.6 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.75 / Num. unique all: 2687 / Rsym value: 28.2 / % possible all: 73.3 |
Reflection | *PLUS Num. obs: 34216 / Num. measured all: 68287 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→65.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1102364.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target using amplitudes
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.21 Å2 / ksol: 0.3656 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→65.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.353 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.309 |