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Yorodumi- PDB-4myb: Crystal Structure of Francisella tularensis 2-C-methyl-D-erythrit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4myb | ||||||
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Title | Crystal Structure of Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) | ||||||
Components | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / alpha and beta protein / nucleotide-diphospho-sugar transferases | ||||||
Function / homology | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / : Function and homology information | ||||||
Biological species | Francisella tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Noble, S.M. / Tsang, A.K. / Couch, R.D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) Authors: Noble, S.M. / Tsang, A.K. / Couch, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4myb.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4myb.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 4myb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/4myb ftp://data.pdbj.org/pub/pdb/validation_reports/my/4myb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 29455.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: ispD, FTL_1525 / Production host: Escherichia coli (E. coli) References: UniProt: Q2A280, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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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 | Density Matthews: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M citric acid, pH 4.5, 7% PEG6000, 0.5 M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2011 / Details: bent conical Si mirror (Rh coated) |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30.562 Å / Num. all: 13737 / Num. obs: 13737 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 42.06 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.068 / Net I/σ(I): 12.35 |
Reflection shell | Resolution: 2.4→2.58 Å / Redundancy: 43 % / Mean I/σ(I) obs: 8.06 / Num. unique all: 1742 / Rsym value: 0.068 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.562 Å / Occupancy max: 1 / Occupancy min: 0.67 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 28.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.29 Å2 / Biso mean: 73.974 Å2 / Biso min: 26.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30.562 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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