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Yorodumi- PDB-3lqu: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lqu | ||||||
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Title | Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase complexed with Ribulose-5 phosphate | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / DHBPS / R5P / ribB / 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 / MOLECULAR REPLACEMENT / Resolution: 2.522 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 | 3lqu.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lqu.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lqu_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 3lqu_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 3lqu_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3lqu_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/3lqu ftp://data.pdbj.org/pub/pdb/validation_reports/lq/3lqu | HTTPS FTP |
-Related structure data
Related structure data | 3lrjC 3ls6C 1g57S 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
#1: Protein | Mass: 23335.439 Da / Num. of mol.: 2 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: Sugar | ChemComp-5SP / | #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: 2.05 Å3/Da / Density % sol: 40.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 8000, 100mM MES-Na, 0.2M Ammonium Salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2009 / Details: Osmic VariMax |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→50 Å / Num. all: 12300 / Num. obs: 12279 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 7.85 |
Reflection shell | Resolution: 2.52→2.61 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.01 / Num. unique all: 1112 / Rsym value: 0.487 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G57 Resolution: 2.522→19.53 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 27.57 / 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: 49.553 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.522→19.53 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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