[English] 日本語
Yorodumi- PDB-1g58: CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g58 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE GOLD DERIVATIVE | ||||||
Components | 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE | ||||||
Keywords | ISOMERASE / dihydroxybutanone phosphate synthase / riboflavin biosynthesis / skeletal rearrangement / antimicrobial target / structure-based design | ||||||
Function / homology | Function and homology information 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Liao, D.-I. / Calabrese, J.C. / Wawrzak, Z. / Viitanen, P.V. / Jordan, D.B. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Authors: Liao, D.I. / Calabrese, J.C. / Wawrzak, Z. / Viitanen, P.V. / Jordan, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g58.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g58.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/1g58 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/1g58 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a homodimer. The two molecules in the asymmetric unit represent the biological assembly. The dimer has a 2-fold symmetry. |
-Components
#1: Protein | Mass: 23335.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET24D(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A7J0, Isomerases; Intramolecular transferases; Transferring other groups #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.47 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0227 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 1999 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0227 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25 Å / Num. all: 72930 / Num. obs: 486817 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.5 / Num. unique all: 3629 / % possible all: 100 |
Reflection | *PLUS Num. obs: 72930 / Num. measured all: 486817 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.55→25 Å / σ(F): 2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→25 Å
| ||||||||||||||||||||
Refine LS restraints |
|