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Yorodumi- PDB-1jxh: 4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jxh | ||||||
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Title | 4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium | ||||||
Components | PHOSPHOMETHYLPYRIMIDINE KINASE | ||||||
Keywords | TRANSFERASE / thiD / ribokinase family / phophorylation / kinase | ||||||
Function / homology | Function and homology information hydroxymethylpyrimidine kinase / phosphooxymethylpyrimidine kinase / hydroxymethylpyrimidine kinase activity / phosphomethylpyrimidine kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Cheng, G. / Bennett, E.M. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution. Authors: Cheng, G. / Bennett, E.M. / 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 | 1jxh.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxh.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxh ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxh | HTTPS FTP |
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-Related 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: 31272.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: thiD / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P55882, phosphooxymethylpyrimidine kinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.3→25 Å / Num. all: 38761 / Num. obs: 38761 / % possible obs: 99.3 % / Redundancy: 7 % / Rsym value: 0.063 / Net I/σ(I): 8.3 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 25741 / % possible obs: 99.9 % / Num. measured all: 177754 / Rmerge(I) obs: 0.063 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.7103 Å2
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Refine analyze | Luzzati sigma a free: 0.36 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.235 / Rfactor Rfree: 0.275 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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