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Yorodumi- PDB-1g57: CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g57 | ||||||
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Title | CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE | ||||||
Components | 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE | ||||||
Keywords | ISOMERASE / dihydroxybutanone phosphate synthase / riboflavine 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: 1.4 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g57.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g57.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/1g57 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/1g57 | 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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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 | ChemComp-CS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: CsCl, Cs(formate), Bis-Tris-propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.93218 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 9, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93218 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→25 Å / Num. all: 93842 / Num. obs: 1025357 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 45.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 10 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 10.9 / Num. unique all: 4666 / % possible all: 100 |
Reflection | *PLUS Num. obs: 93842 / Num. measured all: 1025357 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→25 Å / σ(F): 2 / Stereochemistry target values: TNT library
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Refinement step | Cycle: LAST / Resolution: 1.4→25 Å
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Refine LS restraints |
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