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Yorodumi- PDB-3lrj: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lrj | ||||||
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Title | Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate ion. | ||||||
Components | 3,4-Dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / ENZYME-SULFATE COMPLEX / ALPHA+BETA BARREL / DRUG TARGET / antibacterial / Metal-binding / Riboflavin biosynthesis | ||||||
Function / homology | Function and homology information GTP cyclohydrolase II activity / 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 / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Kumar, P. / Karthikeyan, S. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2. Authors: Kumar, P. / Singh, M. / Gautam, R. / Karthikeyan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lrj.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lrj.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 3lrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lrj_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 3lrj_full_validation.pdf.gz | 485.5 KB | Display | |
Data in XML | 3lrj_validation.xml.gz | 31 KB | Display | |
Data in CIF | 3lrj_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrj ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrj | HTTPS FTP |
-Related structure data
Related structure data | 3lquC 3ls6C 1g57S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 23335.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ribB, STM3195 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P66032, 3,4-dihydroxy-2-butanone-4-phosphate synthase #2: Chemical | ChemComp-SO4 / #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: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 8000, 100mM MES, 0.2M Ammonium sulphate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97869 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 16185 / Num. obs: 15424 / % possible obs: 88.73 % / Observed criterion σ(F): 1.98 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 41.55 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.064 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2259 / Rsym value: 0.21 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G57 Resolution: 2.803→48.909 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.98 / σ(I): 2 / Phase error: 30.11 / 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 / Bsol: 41.257 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 0.5935 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→48.909 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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