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Yorodumi- PDB-4s28: Crystal structure of Arabidopsis thaliana ThiC with bound aminoim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s28 | ||||||
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Title | Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Fe | ||||||
Components | Phosphomethylpyrimidine synthase, chloroplastic | ||||||
Keywords | LYASE / Alpha-Beta Barrel / Radical SAM superfamily / Iron-sulfur cluster / Thiamin / Vitamin B1 / Vitamin B12 / Domain swapping / AdoMet and Glutamate mutase | ||||||
Function / homology | Function and homology information phosphomethylpyrimidine synthase / response to vitamin B1 / carbon-carbon lyase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / plastid / chloroplast stroma / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding ...phosphomethylpyrimidine synthase / response to vitamin B1 / carbon-carbon lyase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / plastid / chloroplast stroma / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding / protein domain specific binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å | ||||||
Authors | Fenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Nat Commun 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s28.cif.gz | 258.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s28.ent.gz | 204 KB | Display | PDB format |
PDBx/mmJSON format | 4s28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4s28_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4s28_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4s28_validation.xml.gz | 26 KB | Display | |
Data in CIF | 4s28_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s28 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s28 | HTTPS FTP |
-Related structure data
Related structure data | 4s25C 4s26C 4s27C 4s29C 4s2aC 4n7qS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64670.090 Da / Num. of mol.: 1 / Fragment: UNP residues 72-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: THIC, PY / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O82392, phosphomethylpyrimidine synthase |
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-Non-polymers , 7 types, 556 molecules
#2: Chemical | ChemComp-SF4 / | ||
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#3: Chemical | ChemComp-AIR / | ||
#4: Chemical | ChemComp-SAH / | ||
#5: Chemical | ChemComp-FE2 / | ||
#6: Chemical | ChemComp-CL / | ||
#7: Chemical | #8: 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: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Na acetate, pH5.3-5.6, 1-9%(v/v) 1,4 butanediol, pH 5.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. all: 158608 / Num. obs: 158556 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 9.91 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4N7Q Resolution: 1.25→40.986 Å / SU ML: 0.07 / σ(F): 1.37 / Phase error: 10.89 / 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 mean: 15.9927 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→40.986 Å
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Refine LS restraints |
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LS refinement shell |
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