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- PDB-4s2a: Crystal structure of Caulobacter crescentus ThiC with Fe4S4 clust... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4s2a | ||||||
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Title | Crystal structure of Caulobacter crescentus ThiC with Fe4S4 cluster at remote site (holo form) | ||||||
![]() | Phosphomethylpyrimidine synthase![]() | ||||||
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Function / homology | ![]() 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E. | ||||||
![]() | ![]() Title: Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Authors: Fenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S.H. / Begley, T.P. / Ealick, S.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.9 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4s25C ![]() 4s26C ![]() 4s27C ![]() 4s28C ![]() 4s29C ![]() 3epnS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | ![]() Mass: 68251.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9A6Q5, ![]() |
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#2: Chemical | ChemComp-SF4 / ![]() |
#3: Chemical | ChemComp-PO4 / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 140 mM HEPES, pH 9.2, and 7.5% (w/v) PEG8000, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.93→50 Å / Num. all: 13706 / Num. obs: 13613 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 5.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3EPN Resolution: 2.93→45.55 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.04 / Stereochemistry target values: ML Details: WEAK RESIDUAL ACTIVE SITE ELECTRON DENSITY IS CONSISTENT WITH LOW OCCUPANCYHMP-P, WHICH WAS NOT ADDED DURING CRYSTALLIZATION BUT WHICH COPURIFIES WITH THE ENZYME. A PHOSPHATE WAS INCLUDED IN ...Details: WEAK RESIDUAL ACTIVE SITE ELECTRON DENSITY IS CONSISTENT WITH LOW OCCUPANCYHMP-P, WHICH WAS NOT ADDED DURING CRYSTALLIZATION BUT WHICH COPURIFIES WITH THE ENZYME. A PHOSPHATE WAS INCLUDED IN THE MODEL, BUT NOT THE PYRIMIDINE
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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 mean: 26.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→45.55 Å
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Refine LS restraints |
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LS refinement shell |
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