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- PDB-1n1d: Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n1d | ||||||
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Title | Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol | ||||||
![]() | glycerol-3-phosphate cytidylyltransferase | ||||||
![]() | TRANSFERASE / alpha/beta fold / cytidylyltransferase / nucleotidyltransferase / negative cooperativity / CDP-glycerol | ||||||
Function / homology | ![]() glycerol-3-phosphate cytidylyltransferase / glycerol-3-phosphate cytidylyltransferase activity / teichoic acid biosynthetic process / cell wall organization / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pattridge, K.A. / Weber, C.H. / Friesen, J.A. / Sankar, S. / Kent, C. / Ludwig, M.L. | ||||||
![]() | ![]() Title: Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis Authors: Pattridge, K.A. / Weber, C.H. / Friesen, J.A. / Sanker, S. / Kent, C. / Ludwig, M.L. #1: ![]() Title: A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis Authors: Weber, C.H. / Park, Y.S. / Sanker, S. / Kent, C. / Ludwig, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cozS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15295.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P27623, glycerol-3-phosphate cytidylyltransferase #2: Chemical | #3: Chemical | ChemComp-C2G / [ #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 38.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 3350, lithium sulfate, Tris, EDTA, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 1998 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→99 Å / Num. all: 40625 / Num. obs: 40625 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.051 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.8→1.87 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.191 / % possible all: 82.1 |
Reflection | *PLUS Num. obs: 40610 / Num. measured all: 121437 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 82.1 % / Rmerge(I) obs: 0.191 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1COZ Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 12.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Num. reflection obs: 40610 / Num. reflection Rfree: 2032 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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