+Open data
-Basic information
Entry | Database: PDB / ID: 1i8d | ||||||
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Title | CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE | ||||||
Components | RIBOFLAVIN SYNTHASE | ||||||
Keywords | TRANSFERASE / riboflavin synthase / riboflavin biosynthesis / antimicrobial target / structure-based design / Escherichia coli | ||||||
Function / homology | Function and homology information riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Liao, D.-I. / Wawrzak, Z. / Calabrese, J.C. / Viitanen, P.V. / Jordan, D.B. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Crystal structure of riboflavin synthase. Authors: Liao, D.I. / Wawrzak, Z. / Calabrese, J.C. / 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 | 1i8d.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i8d.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i8d_validation.pdf.gz | 388.3 KB | Display | wwPDB validaton report |
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Full document | 1i8d_full_validation.pdf.gz | 417.9 KB | Display | |
Data in XML | 1i8d_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1i8d_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i8d ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i8d | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 homo trimer. The three molecules in the asymmetric unit represent the biological assembly. The trimer is asymmetrical. |
-Components
#1: Protein | Mass: 23472.885 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BACTERIA / Plasmid: PET-24A(+) (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P29015, UniProt: P0AFU8*PLUS, riboflavin synthase #2: 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: 2.51 Å3/Da / Density % sol: 50.94 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: bis-tris propane, MgCl2, diglyme, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: 1.1271 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 48686 / Num. obs: 437196 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 5 % / Rmerge(I) obs: 0.215 / % possible all: 96.7 |
Reflection | *PLUS Num. obs: 48686 / Num. measured all: 437196 |
Reflection shell | *PLUS % possible obs: 96.7 % / Mean I/σ(I) obs: 5.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→25 Å / σ(F): 2 / Stereochemistry target values: TNT library
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.239 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.99 |