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Yorodumi- PDB-5ddt: Crystal structure of IspD from Bacillus subtilis at 1.80 Angstrom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ddt | ||||||
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Title | Crystal structure of IspD from Bacillus subtilis at 1.80 Angstroms resolution, crystal form I | ||||||
Components | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
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 Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jin, Y. / Liu, Z.C. / Wang, G.G. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis. Authors: Jin, Y. / Liu, Z. / Li, Y. / Liu, W. / Tao, Y. / Wang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ddt.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ddt.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ddt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/5ddt ftp://data.pdbj.org/pub/pdb/validation_reports/dd/5ddt | HTTPS FTP |
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-Related structure data
Related structure data | 5ddvC 5hs2C 2yc3S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 25879.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: ispD, yacM, BSU00900 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) References: UniProt: Q06755, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M Trimethylamine N-oxide dehydrate, 0.1M Tris, pH 8.5, 20% (v/v)Polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→60 Å / Num. obs: 42387 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YC3 Resolution: 1.8→59.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.971 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.023 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→59.33 Å
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